5QJX
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z2856434778
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293.15 | 33 % PEG4k, 0.2 MgCl2 and 0.1 M Tris |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.52 | α = 79.68 |
b = 59.52 | β = 82.36 |
c = 80.62 | γ = 76.36 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2018-07-28 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.91587 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||
1 | 1.73 | 57.16 | 96.4 | 0.051 | 0.072 | 0.051 | 0.993 | 8.9 | 1.8 | 86383 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.73 | 1.77 | 95.8 | 0.623 | 0.882 | 0.623 | 0.699 | 1.8 | 6385 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | THROUGHOUT | 6GRU | 1.73 | 78.96 | 82072 | 4310 | 96.31 | 0.2222 | 0.2204 | 0.2564 | RANDOM | 37.89 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
3.41 | 0.4 | 1.83 | -0.62 | 1.61 | -1.58 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.486 |
r_dihedral_angle_4_deg | 15.859 |
r_dihedral_angle_3_deg | 14.232 |
r_dihedral_angle_1_deg | 7.085 |
r_mcangle_it | 4.875 |
r_mcbond_other | 3.631 |
r_mcbond_it | 3.63 |
r_angle_refined_deg | 1.89 |
r_angle_other_deg | 1.03 |
r_chiral_restr | 0.114 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5713 |
Nucleic Acid Atoms | |
Solvent Atoms | 226 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
REFMAC | phasing |