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Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound
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 2.19 43.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.769 α = 90 b = 87.869 β = 97.44 c = 73.243 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 2M 2023-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95370 CLSI 08ID-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 1.62 50 97.1 0.106 0.115 0.044 0.995 8 6.6 76756
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 1.62 1.65 86.1 0.751 0.827 0.339 0.769 5.1
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 FOURIER SYNTHESIS THROUGHOUT 1.62 43.97 72980 3750 96.39 0.14983 0.14789 0.1595 0.18727 0.1902 RANDOM 20.418
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] -0.19 0.56 0.1 -0.05
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.819 r_dihedral_angle_3_deg 11.987 r_long_range_B_other 11.875 r_dihedral_angle_1_deg 7.454 r_scangle_other 7.172 r_mcangle_it 6.333 r_mcangle_other 6.333 r_dihedral_angle_2_deg 4.624 r_scbond_it 4.574 r_scbond_other 4.573
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.819 r_dihedral_angle_3_deg 11.987 r_long_range_B_other 11.875 r_dihedral_angle_1_deg 7.454 r_scangle_other 7.172 r_mcangle_it 6.333 r_mcangle_other 6.333 r_dihedral_angle_2_deg 4.624 r_scbond_it 4.574 r_scbond_other 4.573 r_mcbond_it 3.979 r_mcbond_other 3.978 r_rigid_bond_restr 2.252 r_angle_refined_deg 1.338 r_angle_other_deg 0.482 r_chiral_restr 0.069 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 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 4656 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling REFMAC phasing HKL-3000 data reduction