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Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 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, HANGING DROP 293 20% PEG3350, 0.2M di-Ammonium Citrate
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.865 α = 90 b = 88.084 β = 97.56 c = 73.562 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 16M 2022-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.55 50 98.4 0.065 0.072 0.031 0.999 27.6 5.3 88118
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 98.7 0.748 0.795 1.88 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PXW 1.55 44.08 86348 1744 98.17 0.1818 0.18123 0.20898 0.2335 RANDOM 22.966
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] 0.83 -1.5 0.12 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.761 r_dihedral_angle_3_deg 12.096 r_dihedral_angle_4_deg 11.698 r_dihedral_angle_1_deg 7.822 r_long_range_B_refined 4.956 r_long_range_B_other 4.917 r_scangle_other 3.492 r_mcangle_other 2.79 r_mcangle_it 2.789 r_scbond_it 2.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.761 r_dihedral_angle_3_deg 12.096 r_dihedral_angle_4_deg 11.698 r_dihedral_angle_1_deg 7.822 r_long_range_B_refined 4.956 r_long_range_B_other 4.917 r_scangle_other 3.492 r_mcangle_other 2.79 r_mcangle_it 2.789 r_scbond_it 2.249 r_scbond_other 2.248 r_mcbond_it 1.766 r_mcbond_other 1.765 r_angle_refined_deg 1.421 r_angle_other_deg 1.368 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4620 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 71
Software Software Software Name Purpose HKL-3000 data scaling PHASER phasing REFMAC refinement HKL-3000 data reduction