5LBW
Structure of the human quinone reductase 2 (NQO2) in complex with volitinib
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5LBU |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 200 mM sodium sulphate, 2.2 M ammonium sulphate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.32 | 46.98 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 57.398 | ¦Á = 90 |
b = 81.372 | ¦Â = 90 |
c = 106.403 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2015-11-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 0.979 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.9 | 44.5 | 90 | 0.11 | 0.996 | 7.49 | 4.7 | 36213 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.9 | 1.97 | 93 | 0.97 | 1.3 | 4 |
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 | 5LBU | 1.9 | 44.5 | 34410 | 1803 | 90.5 | 0.25404 | 0.25317 | 0.2705 | RANDOM | 42.198 |
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] | |
8.01 | -2.77 | -5.24 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.722 |
r_dihedral_angle_4_deg | 13.944 |
r_dihedral_angle_3_deg | 12.839 |
r_dihedral_angle_1_deg | 6.189 |
r_long_range_B_refined | 2.888 |
r_long_range_B_other | 2.887 |
r_angle_refined_deg | 1.317 |
r_angle_other_deg | 0.896 |
r_scangle_other | 0.481 |
r_mcangle_it | 0.478 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3608 |
Nucleic Acid Atoms | |
Solvent Atoms | 39 |
Heterogen Atoms | 160 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
REFMAC | phasing |