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Crystal structure of the WDR domain of human DCAF1 in complex with OICR-39512 compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG3350, 0.2 M Magnesium formate
Crystal Properties Matthews coefficient Solvent content 3.21 61.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.34 α = 90 b = 82.34 β = 90 c = 233.617 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER X 16M 2023-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 1.8 50 99.9 0.063 0.065 0.018 1 6.3 13.7 44430
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 1.8 1.83 99.9 0.95 0.985 0.258 0.871 14.3
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 45.22 42962 1377 99.89 0.15759 0.15654 0.1738 0.19136 0.2009 RANDOM 28.3
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] 0.23 0.11 0.23 -0.74
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.732 r_long_range_B_other 15.199 r_dihedral_angle_3_deg 12.034 r_scangle_other 10.945 r_mcangle_other 9.528 r_mcangle_it 9.524 r_dihedral_angle_1_deg 7.501 r_scbond_it 7.226 r_scbond_other 7.218 r_dihedral_angle_2_deg 6.613
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.732 r_long_range_B_other 15.199 r_dihedral_angle_3_deg 12.034 r_scangle_other 10.945 r_mcangle_other 9.528 r_mcangle_it 9.524 r_dihedral_angle_1_deg 7.501 r_scbond_it 7.226 r_scbond_other 7.218 r_dihedral_angle_2_deg 6.613 r_mcbond_it 6.24 r_mcbond_other 6.203 r_rigid_bond_restr 2.927 r_angle_refined_deg 1.271 r_angle_other_deg 0.452 r_chiral_restr 0.068 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2374 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing