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Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SSE
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 2.22 44.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.954 α = 90 b = 88.41 β = 97.86 c = 73.556 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 S 6M 2023-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18061 CLSI 08B1-1
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 1.56 50 98.1 0.043 0.048 0.02 1 11.2 5.2 86595
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 1.56 1.59 82 0.585 0.675 0.329 0.566 3.7
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 1.56 38.83 82353 4204 98.02 0.16863 0.16659 0.1908 0.20798 0.2219 RANDOM 25.77
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] -3.49 -1.69 4.37 -0.4
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.253 r_long_range_B_other 16.541 r_dihedral_angle_3_deg 12.226 r_scangle_other 11.008 r_mcangle_other 10.938 r_mcangle_it 10.937 r_rigid_bond_restr 8.484 r_dihedral_angle_1_deg 8.007 r_dihedral_angle_2_deg 7.991 r_scbond_it 7.804
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 17.253 r_long_range_B_other 16.541 r_dihedral_angle_3_deg 12.226 r_scangle_other 11.008 r_mcangle_other 10.938 r_mcangle_it 10.937 r_rigid_bond_restr 8.484 r_dihedral_angle_1_deg 8.007 r_dihedral_angle_2_deg 7.991 r_scbond_it 7.804 r_scbond_other 7.802 r_mcbond_it 7.783 r_mcbond_other 7.782 r_angle_refined_deg 1.363 r_angle_other_deg 0.488 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 4639 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling REFMAC phasing PDB_EXTRACT data extraction HKL-3000 data reduction