Questions related to X-ray Crystallography
I divided two compounds and found that when their absolute configuration at the 7-position is(R), the C-7 carbon spectrum data is 38.6, and the C-8 carbon spectrum data is 26.7; when the absolute configuration of the 7-position is(S), the C-7 carbon spectrum data is 37.4, and the C-8 carbon spectrum data is 27.1. The absolute configuration of C-7 was determined from single-crystal X-ray crystallography.
Greetings all scientist!!
I would like to know, which is the best software for Rietveld refinement among FullProf vs Rietan FP.
Thank you all for Your wonderful opinions in advance.
Hello all, this is a 2Fo - Fc and Fo - Fc map of my protein - ligand complex (the R-free is 0.4464), and I can't find out what the hollow electron density map in the center is.
Since the Fo - Fc in that area is 0, I assume that there is no ligand.
However the 2Fo - Fc is still positive with no structure inside!
Is that a noise? Or is it a consequence of a low R-free value?
I have a dataset from x-ray crystallography that is has poor statistics from processing (high Rmerge) and does not refine particularly well. I ran the merged reflections through Xtriage (Phenix) and the program tells me that my space group may be incorrect and suggests that I try merging in lower symmetry.
I have done very little manipulation of the files that go in to scaling and processing before, so I'm not sure how I can use XDS to merge in lower symmetry. Usually, I use the processed file from XDS coming off the beamline with no problem, but not this time!
Any help in figuring out how to do this would be much appreciated.
I'm now synthesizing some ruthenium(II) tris(heteroleptic) complexes with the anion hexafluorophosphate.
However, when I'm trying to grow crystals for my complexes, several common solvent pairs (ACN/ether, MeOH/ether, THF/ether ......) does not provide me fine crystals.
Recently, I've found that some research use the solvent pairs Acetone/H2O or MeOH/H2O, and I would like to try the solvent pairs.
Therefore, I'm wondering how I can grow crystals from these solvent pairs? Since water does not evaperate easily for the slow diffusion method, and the density of water is too large for the bilayer method.
Do anyone have experiences using these solvent pairs? Or can anyone give me some suggestions in recrystallization? Thanks!
Can anyone please explain which type of structure is preferred for a ligand-Receptor docking study? When both the NMR based and X ray crystallography based structures both are available in PDB?
When solving the phase problem in x-ray crystallography using the heavy atom isomorphic replacement method, we cannot calculate the patterson function for the protein structure factor and instead calculate it for the heavy atom structure factor. However, why is it that we can calculate the patterson function for the protein structure factor without problems in the molecular replacement method?
After the synthesis of a compound at the mono Crystal form I process by structural determination. I ground the product and passed in XRD powder, when I calculated the distance and the lattice planes with HKLgen (using the cell parameters found for the single crystal), I cannot index my spectrum powder? (I did the same for three other hybrid compounds is always the same).
At present I am working on low valent metal complexes. I am intended to determine their structures by X- ray crystallography. Therefore it would be helpful for me if you answer me the most appropriate methods of crystallization of low valent metal complexes to grow single crystals suitable for XRD.
I am depositing indium oxide thin film (30 nm) and nano wire (200 nm) on p-type Si substrate using E-beam evaporator. I took the XRD Measurement so i want to know how to calculate d-spacing and lattice constant and what information we will get from d-spacing and lattice constant about the structure. Even i want to know through XRD peak how we can analyse whether it is bcc- cubic or simple cubic (Manually, without comparing withJCPDS File, is there any manual way). I am attaching XRD Measurement file. The XRD peaks are 211/ at 21 (degree) , 222/ 33(deg) ,622 / 62(deg) , 032/ 69 (deg).
I am not sure whether crystalexplorer is corrupted or not? I have tried to open .cif file downloaded the Crystallography Open Database, but still can't open it ? I hereby attach this file and please do check it. if it works well, please advise how I can perform hirshfeld surface analysis?
I have some molecules with known crystallography data (cif file) I wanted to calculate the EXANES and XANES for the material.
please suggest me the best way ?
I have tried every combination of parameter changes and after that i have a poor chi square value. I can't get it lower any further. I know there have been a lot of discussion about Rietveld refinement but i can not find any solution for my case. Any insight will be appreciated.
i synthesized aromatic schiff base from 3-aryl-5-amino 1,2,4-triazol. How can i know it is E or Z using another tool than X ray crystallography.
AF2 may most strongly impact experimental determination of protein structure by multiple methods with possible benefits and negative impacts over time.
Some areas may need to quickly pivot or become obsolescent, whereas other may thrive.
Structures of large macromolecular machines should be enabled by having accurate computational structures for subunits and components.
The already great value of sequence data (which is doubling every 8 months) is likely to become far greater by being more directly connected to spatial information.
Overall the pace of biology and biophysical advances can be expected in increase by the ability to better harness the flood of sequence data.
What do you think?
An interstitial atom (such as H, N, O) sitting not on their regular place, but between other atoms in the metals structure.
How to detect where is their location on that structure (in crystallographic viewpoints) with instrument analysis rather than assumed.
there are a number of textbooks available for studying x-ray crystallography by targeting Structural Biology and some of them are definitely excellent. I just want to pick one single textbook which will cover all of the aspects of the x-ray crystallography. As a novice which one will be perfect or at least suitable for me? Please give me your suggestion.
I am refining the crystal structure of a protein that is around 20 kDa. I am getting towards the point where most of the validation statistics and residual look nice: resolution 1.85Å, Rfree=19.5% Rwork=15.5%, Angle and bonds RMS below 0.01Å respectively 1.1˚, mol probity score < 1.1, No Ramachandran outliers and over 98% of Ramachandran favoured, no C-beta outliers, very low clashscore. There are a few rotamer that still need a little bit of attention. After correcting them manually with Coot I usually follow with a short round of refinement (3 macro cycles) with Phenix.refine using the following parameters:
Real space position (XYZ), TLS, individual B-factors and both X-ray /stereochemistry and X-ray ADP weight optimisation. Unfortunately The R-stats always get worse (e.g. +1% for R-free) while the geometry (angle and bond) marginally improves if at all. The rotamers that I have just corrected are often back to the wrong position. Basically my model gets worse. I have played around with the different parameters but I always end up with the same problem. What is the best refinement strategy in this kind of situation? I was wondering if there is a way to tell phenix to make minimal changes to most of the structure and only focus on the area that I have recently modified. I would be keen to learn how to play with Phenix a little more efficiently.
Your help is much appreciated.
I have been trying to synthesize Grephene Quantum dots using graphite using microwave assisted disintegration.
I know that x-ray crystallography can be used, and various applications of electron microscopy. however are there any others. I was thinking maybe immunoprecipitation followed by western blotting?
I have a protein crystal structure at 1.83 angstroms with 2 molecules in the asymmetric unit. But the B factor of the second molecule is almost twice as large as the first. After running ARP/wARP , the first protein molecule is built in but only 50% of the second molecule is built into the electron density. It appears that I somehow have weak or missing reflections for the second protein molecule. How can this be?
I have a good quality x-ray powder diffraction pattern. For indexing, I tried different software, However, I am sure it can also be done more easily with TOPAS academic version. I know how to search peak with Le bail but I could not apply any indexing algorithms such as ITO etc. in TOPAS. I also use Jedit interface.
I could not find any good material or example on internet. I would be really appreciate if any one can help me or send me a tutorial link.
#XRD #Indexing #TOPAS #crystallography #mineralogy
If i repeat a sample at different scanning rate on same instrument, then is there any chance that there will be a shift in peak positions or change in Intensity?
1) It’s known that x-ray crystallography is better than NMR or homology modeling;
2) Also, it’s known that adaptable resolution (<2 A) is better;
3) And the target should not have missing residues; [how can I know about this criteria?]
By searching PDB, many of the results (in my case, all of them) are x-ray diffraction, and many of them are in adaptable resolution.
In my case, searching «phosphodiesterase-5» resulted in 30 items in humans.
How can I select the best one for docking?
Please aid with software as well as strategies in order to get X-ray structure in a similar fashion to single crystal X-ray refinement. We have D2 Phaser-Bruker XRD instrument to obtain PXRD data available. Thanks in advance
In several screens, I saw some crystals that look like protein crystals, but they redissolved and became unapparent during checking them under light microscopy after a few seconds.
For example, in a buffer screen containing 30%v/v PEG400,100mM Tris/HCl and 200mM Li2SO4, a rather big (~0.1mm) triangular star-like crystal became unapparent after about 1 minute.
It is really possible for protein or salt crystals? In the reservoir buffer of this screen, there were several plate-like crystals seeming to be Li2SO4 crystals or PEG400! These were different from the crystals in drop.
I am wondering whether the PEG prepared from powder is suitable for crystallisation purpose. As I read from the product speciation of PEG produced by Hampton Research, it mentioned that it is produced for crystallisation uses and it is monodisperse. Hence, I am wondering whether the PEG prepared by ourselves from powder is carrying the same properties.
If the N-terminal region of a protein is known to be very flexible because it doesn't have a good electron density when doing X-ray crystallography, will a His6-tag be expected to affect its activity?
Given the different quality metrics for protein models based on XRD and NMR data, I want to know your opinon.
In particular, how good is the agreement between NMR and XRD-derived structures? In case of disagreement, which method would your trust better (assuming both were reasonably conducted)?
When facing the solution of a structure de novo, how is the method chosen? How much does it cost to solve a structure by X-ray compared to NMR?
Thank you very much for your insights!
Minor lab has recently published this article covering practical aspects or crystallographic model refinement (
Our own rules, guidelines, and tips have changed over time due to increased experience and the perpetual evolution of crystallographic software. Moreover, we understand that some crystallographers might disagree with certain suggestions presented in the article. We are always open to discussion on best practices, and I would love to hear feedback, comments, and further suggestions.
If you don’t have an institutional access, please use this link https://www.tandfonline.com/eprint/3UyYh3iNGfhTSJGXyz9K/full (it has a limited number of free copies).
I am working on two proteins of the UPS, that have been shown to interact with each other in vivo. The ultimate goal is to study the complex using X-ray crystallography. I would also like to study if this interaction is direct or mediated by other protein partners.
So far I have not been successful in establishing the interaction in vitro. If I purify the proteins separately and put them together for crystallization, will this help in anyway?
I have also tried performing Co-immunoprecipitation experiments in vivo and check for potential interaction partners using MS analysis, but this has not panned out either.
I would be grateful if anyone has inputs or suggestions as to how i can take this ahead. Thanks in advance!
As per the underlying concept of this new theory, when X-rays are scattered from tiny crystals or crystallites of any size and shape distributed throughout space, the diffraction pattern will contain enhanced scattering at angles of exactly equal to 2θB, whatever the orientation of the crystal. Thus it is claimed that scattering from a randomly oriented crystal powder with gives rise to Bragg scattering peaks even if the Bragg condition of individual crystallite is not satisfied.
Do you agree ?
What is your opinion?
i have the XRD data of a rock sample. i want to know the % of its constituent minerals and percentage of clay it contain....how can i do this using Xpert high score plus....?
We've looked at an epitaxial film of GaN on a Si substrate using real time 2D Bragg XRD Microscopy (2D XRD rocking curve analysis). This specimen also had intermediate "buffer" layers of AlxGa1-xN and AlN. The XRD rocking curve Bragg profiles were examined at various topographic locations. The (0002)s reflection was utilized. The vicinity of the GaN (0002)s reflection was probed in reciprocal space using the ω-2ϴ scan mode to acquire the Bragg profiles.
We need some help! We're on the verge of a solution. Check out this data set and analyses for a GaN-AlxGa(1-x)N-AlN-Si sample wafer. I have the 3D XRD rocking curve data collected using a commonly available lab based XRD instrument below 2kW. I have the relative intensities for five distinct Bragg peaks around the GaN (0002)s reflection.
ok so i know that it depends oon the radiation of the excitor. but i really want to know why does it happen and how does it happen. All the answers will be highly appreciated.
Conformational properties of porphyrins have an importance in biological systems.
what are the factors that determine porphyrin conformation (planar or non planar)?
I am not a crystal structural biologist. I have few questions that could be rather technical. I am aware that there are some proteins that are difficult to study using x-ray crystalllography (e.g small heat shock proteins). What about these proteins that make them hard to study using x-ray crystallography? What are some other general features that makes a protein hard to study using x-ray crystallography? Also if there are some brief reasons at the level of fundamental principles, please feel free to let me know.
Hi, I used Apex-3 for structure determination and XShell for refinement for one crystal structure. The generated CIF file has one major Alert A; Large Value of Not (SHELXL) Weight Optimized S. I do not have much experience to solve these issues. Also, how can I omit reflections that have error/sigma values greater than 10 in the refinement.
In addition, how can I examine the LST file for refinements to check the Most Disagreeable Reflections list for possible reflections to omit.
Hi... I am working on a viral protein. When I purify it in the normal condition (Tris buffer, pH-7.5, NaCl & Glycerol, Temp- 4C), it is a monomer. But, as its crystal structure reveals, upon crystallization (pH-6.5, Temp- 20C) it converts into a crystallographic tetramer. What could be the possible reason behind this morphological transition of the protein ?
Your view would be a subject of appreciation!
In order to calculate the crystallinity of a polycrystalline material (eg. clays), I would like to use XRD. It needs to deconvolute the XRD pattern coming from crystalline part and amorphous part of the material. How can I decompose or deconvolute the XRD graph using PANalytical X pert High score plus, Version 2.0 software.
1. What should be the ideal resolution of a crystal structure, if one wants to compare the B-factors as defined by the structure and anisotropic atomic displacement parameters (ADP) obtained from refinement procedure like Translation-Libration-Screw (TLS).
2. Is it practically correct to refine a set of crystal structures from different research groups by TLS refinement to get a list of ADPs and compare them with the thermal or B-factors reported in PDB files?
All peaks are matching with the jcpds file. All seems to be in single phase, but when I am trying to do Rietveld refinement, the maximum intensity peak is not fitting. I even tried refining preferred orientation parameters, but it is of no use. I am not sure whether it is a different phase or it is a preferred orientation that is causing the problem. Data points are less; please exclude that.
I did Rietveld refinement for my x-ray diffraction data using the GSAS+EXPGUI package. The fit seems to be good. Now i wish to extract the Integrated intensity ( both calculated and observed) of all reflections from GSAS software. I aware of the reflist option in GSAS, but it gives 4 different values (highlited in the attached figure). Can some one explain me, in what way they are different?.
Hi every body
I have synthesized a new material in powder. Absolutely it is polycrystalline not single crystal. I am looking for a way to analyze this XRD pattern? I have read in papers about Refinement of the powder XRD but I don't know too much about it.
How can we analyze the XRD pattern of a new material without synthesizing its single crystal?
Recently we synthesized some CdS particles. Prepared samples were characterized by X-ray diffraction. The ayanlysis result shows a hexagonal structure (ICSD 43599) in space-group of P 63 m c (186). Its cell parameters are a=4.1400 Å and c=6.7150 Å.
I use diamond3.2 opened the ICSD 43599.cif and created several planes on the crystal. I found that in the planes of (100), (101) and (103) there had no atoms presence. Yet in the X-ray diffraction results these three planes all showed diffraction peaks.
My question was: Must the corresponding crystal planes of the X-ray characteristic peaks have atoms present? If it is, why in the crystal models (ICSD 43599.cif) on the (100), (101) and (103) planes I created have no atoms presence; If it is not, why these three planes showed diffraction peaks?
Further more, the question is: did diffraction planes (which showed diffraction peaks) must have atoms presence? And the reasons.
I used MAUD program to analyze my XRD patterns. Many times I noticed that MAUD gives different refinements for the same cif-files if I change the order of them in the phases window. Also, some times I repeat the same phase twicely in the phases window and I notice that each phase starts to has its own persentage and fitting value and may has half of the peaks and the second one has the remaining half of peaks for the same phase. Also, when I make many changes in the structural coordinations of one phase, MAUD stops responding to the change after some tries and may give a strange refinement that will not appear again if I restart the program. Also, using my computer or other computers will give different results for the same procedure in the MAUD program.
1-do you have any experience in using MAUD program?And pleases explain my previous case
2- give me another more accurate program to analyze the XRD results?
I'm trying to refine the structure of double-mutated protein at 2.4 A resolution. For MR I used the structure (not fully refined, 2.75A Res) of the Wild Type. After first round of refinement I got Rwork/Rfree = 0.30/0.35. However, after the successive next rounds of refinement even if the Rwork/Rfreedecresases, the density map fit completely fails. Does anyone have an idea why it happens?
The X-ray data shows severe anisotropy. Do you think that refining B-factors anisotropically may help?
Is this the only way to justify orientation of the crystals? If certain planes are more intense in XRD would that mean that others need to be less intense given that the amount is unchanged?
Thank you for your insights.
I am looking for step by step procedure to find the crystallite size and microstrain by warren-averbach using xpowder and how can we interpret the plots. is this method able to estimate the dislocation density and is there empirical equation to estimate the dislocation density using xrd.
the attached picture is for the analysis using xpowder. in the instrumental profile, how can i find the instrumental broadening and compare it with measured pattern.
looking for help to know much about the correct procedure from your wide experience.
P.S. Can we Use the experimental sample instead of the standard one to estimate the instrumental broadening after annealing.
I am having some difficulties for quatification analysis of Hap in a sample. In our Rietveld software there are 5 different cards for Hydroxyapatite, and they result in different values.
What should I do to choose the right one in order to get a trustable result?
I'm a freshman in the crystallographic field.
Now I have a crystal that have been confirmed as protein, and it looks like a dot without clear edge.
I have tried to optimize the crystallographic condition,like the concentration of precipitant and the pH range of buffer.
but the resolutioin is only 5 Å using X-ray diffraction。
So could you please share your experience to improve the resolution of protein crystal?
Question for X-ray diffraction experts!
Let's assume a structure: layered mineral intercalated with organic long chain molecules. The X-ray diffraction pattern shows 3 peaks connected with 1st, 2nd and 3rd order reflections. Now, the structure is exposed to UV light which changes the conformation (geometry) of the intercalated molecules. After that the d spacing should change (1st order reflection), however we see a change of the 2nd and 3rd order reflection? The 1st order is not "moving". Do you have any suggestions?
I have a cif file of one my compound, in the structural data file there is an atomic oxygen, which is definitely a water. But by the mistake of crystallographer during structure solving, addition of hydrogen on that atom was missed. Now we have lost the structure factor files and we want to insert H-atoms on the said atom.
I have GIXRD data for Ion irradiated Ni sample. I want to calculate domain size and microstrain using Warren–Averbach method. I donot get the option for WA analysis in the calculation tab using MARQX software after reading the input file. Can someone suggest what could be the reason?
I would like to know details about Rietveld Refinement (Prof. Hugo Rietveld) in terms of the application. I have some questions on this technique.
FYI, I'm the user for PANalytical X'pert Pro with software X'pert Highscore Plus.
Normally I will interpret the diffractogram by looking the SemiQuantitative(%). However, for the sample with ratio composition, perhaps by only look at the SemiQuant result is not enough. Therefore, I engage with Rietveld Refinement (Basic) as this feature already included in the software. It seems like the result in terms of composition is make sense and it follow the composition of the sample(Example Graphene+ZnO. 1:1, 1:2, 1:4 and so on)
My question is,
1. How is the accuracy is Rietveld Refinement technique?Is it better than if I'm not using it?
2. How to confirm that Pseudo-Voigt Curves is fitting well under diffractogram curves?
3. How famous this technique to be included in the research?
4. Is there any similar technique or better compared to the Rietveld Refinement?
I am running pw.x calculations for Mo2C (orthorhombic) supercell of size 1x1x3 and 2x2x2. The calculations terminating with an error "Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted". The energy values goes up and down and the structure is not converging towards low energy value. The cell parameters are according to the .cif files (crystallography.net) and updated according to cell size.
However the calculation with 1x1x2 Mo2C works fine without any error. By increasing the cell the above mention error arises. I tried with altering the nbnd, degauss, electron maximum steps, but the problem remains same.
mpirun -np 32 ./pw.x -npool 8 < File.input > File.out
Input file is as follows
calculation = 'relax'
title = 'Mo2C'
verbosity = 'minimal'
wf_collect = .false
nstep = 2000
prefix = 'BP'
ibrav = 0
nat = 36
ntyp = 2
nbnd = 210
ecutwfc = 50
occupations = 'smearing'
degauss = 0.001
smearing = 'methfessel-paxton'/
electron_maxstep = 300
conv_thr = 1D-5
startingpot = 'atomic'
startingwfc = 'atomic'
diagonalization = 'david'
ion_dynamics = 'bfgs'
cell_dynamics = 'bfgs'
cell_dofree = 'z'
Can anyone assist me to solve this error.
Thank you in advance
I read some protocols suggesting not lyophilizing the protein in sample preparation. any practical tips? thanks a lot!
Hi! Currently I have two versions of the same protein, a native one and one in which I added a long flexible tail sequence. They both gave me crystals in the same condition, and by X-ray diffraction patterns they have very close symmetry and cell parameter.
I am wondering if any parameter from X-ray diffraction can show me the clear difference between these two crystals (prove that one of them has tail)? I know solvent % may show that the one with tail has less solvent in channels, but that's still estimated from the molecular weight I provided. Will any other experimental data differ for the two crystals?
Thanks a lot!
We have prepared bulk Gd0.7Sr0.3MnO3 materials by conventional solid state reaction technique. Their corresponding nanoparticles were prepared by using ultrasonic energy. The lattice parameters for the bulk polycrystalline sample and corresponding nanoparticles prepared by ultrasonication are almost unaltered, however, the atomic positions are significantly different between the materials prepared by two different techniques. By using FULLPROF studio we have generated the structural view of Gd0.7Sr0.3MnO3 (a) bulk materials and (b) corresponding as shown in the attached figure. Is it realistic? Please let us know any expert opinion. Thank you very much in advance.
There are values of unit cell as well as transformation matrix to get fractional values of the coordinates. These values are related to only for the structures derived from X-Ray crystallographic method. I wanted to know how it is significant after the structure has already been solved. Are there any calculations/methods/algorithms related to the coordinates where this data is applied?