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Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156
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% PEG 3350, 0.2 M Magnesium formate
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.35 α = 90 b = 88.6 β = 98.01 c = 73.409 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 EIGER X 9M 2023-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95369 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 1.4 50 99.4 0.068 0.074 0.028 0.997 8.6 6.6 121825
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 1.4 1.42 93.3 0.675 0.752 0.323 0.804 4.9
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 1.4 44.34 115828 5964 99.38 0.14724 0.14583 0.1634 0.17423 0.183 RANDOM 15.619
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] 0.5 -0.41 0.09 -0.46
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.708 r_dihedral_angle_3_deg 11.388 r_long_range_B_other 10.38 r_dihedral_angle_1_deg 7.749 r_scangle_other 5.68 r_mcangle_it 5.194 r_mcangle_other 5.194 r_dihedral_angle_2_deg 4 r_scbond_it 3.637 r_scbond_other 3.637
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.708 r_dihedral_angle_3_deg 11.388 r_long_range_B_other 10.38 r_dihedral_angle_1_deg 7.749 r_scangle_other 5.68 r_mcangle_it 5.194 r_mcangle_other 5.194 r_dihedral_angle_2_deg 4 r_scbond_it 3.637 r_scbond_other 3.637 r_mcbond_it 3.212 r_mcbond_other 3.212 r_rigid_bond_restr 2.095 r_angle_refined_deg 1.135 r_angle_other_deg 0.439 r_chiral_restr 0.063 r_gen_planes_refined 0.007 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 4701 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction REFMAC phasing PDB_EXTRACT data extraction