9BHS
Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7SSE |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 291 | 30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 48.442 | α = 90 |
b = 87.884 | β = 96.75 |
c = 73.075 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
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 PILATUS3 2M | 2023-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.2 | 1.000 | ALS | 5.0.2 |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.43 | 50 | 97.3 | 0.045 | 0.049 | 0.019 | 0.999 | 8.9 | 6.6 | 108966 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.43 | 1.45 | 81.7 | 0.463 | 0.511 | 0.21 | 0.898 | 5.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.43 | 42.5 | 103543 | 5396 | 97.14 | 0.14194 | 0.1405 | 0.16957 | RANDOM | 16.638 |
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] | |
1.86 | -0.53 | -1.11 | -0.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_long_range_B_refined | 11.071 |
r_dihedral_angle_3_deg | 11.062 |
r_long_range_B_other | 10.078 |
r_dihedral_angle_1_deg | 7.547 |
r_scangle_other | 5.932 |
r_dihedral_angle_2_deg | 5.77 |
r_mcangle_other | 5.32 |
r_mcangle_it | 5.319 |
r_scbond_it | 3.855 |
r_scbond_other | 3.854 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4698 |
Nucleic Acid Atoms | |
Solvent Atoms | 496 |
Heterogen Atoms | 75 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data scaling |
HKL-3000 | data processing |
HKL-3000 | data reduction |