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Crystal structure of the human DCAF1 WDR domain in complex with OICR-40151
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 30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide
Crystal Properties Matthews coefficient Solvent content 2.21 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.794 α = 90 b = 88.659 β = 97.4 c = 73.394 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 CCD RIGAKU SATURN A200 2023-08-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 1.67 50 97.2 0.076 0.087 0.043 0.996 10 4 69788
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 1.67 1.7 95.1 0.809 0.934 0.461 0.652 3.9
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 1.67 18.76 64893 3368 94.99 0.22045 0.21878 0.2279 0.25295 0.2585 RANDOM 17.924
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] 0.53 -0.77 -0.04 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.953 r_dihedral_angle_2_deg 8.478 r_dihedral_angle_1_deg 8.076 r_long_range_B_refined 5.195 r_long_range_B_other 5.083 r_scangle_other 3.521 r_mcangle_it 2.643 r_mcangle_other 2.643 r_scbond_it 2.205 r_scbond_other 2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.953 r_dihedral_angle_2_deg 8.478 r_dihedral_angle_1_deg 8.076 r_long_range_B_refined 5.195 r_long_range_B_other 5.083 r_scangle_other 3.521 r_mcangle_it 2.643 r_mcangle_other 2.643 r_scbond_it 2.205 r_scbond_other 2.205 r_mcbond_it 1.689 r_mcbond_other 1.689 r_angle_refined_deg 1.391 r_angle_other_deg 0.493 r_chiral_restr 0.072 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4672 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling REFMAC phasing PDB_EXTRACT data extraction HKL-3000 data reduction