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Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102
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 7 291 3.2 M NaCl, 0.1 M Bis-Tris Propane pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.19 43.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.692 α = 90 b = 88.192 β = 97.47 c = 73.099 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 0.9537 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 1.48 50 99.9 0.058 0.064 0.027 0.998 10.1 5.6 103575
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 1.48 1.51 99.9 0.794 0.883 0.38 0.718 5.3
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 1.48 38 98392 5152 98.84 0.15955 0.15779 0.1671 0.19321 0.1962 RANDOM 17.446
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] 0.03 0.02 -1 0.94
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.43 r_dihedral_angle_3_deg 11.116 r_long_range_B_other 10.441 r_dihedral_angle_1_deg 7.546 r_scangle_other 6.266 r_dihedral_angle_2_deg 5.69 r_mcangle_it 5.661 r_mcangle_other 5.66 r_scbond_it 4.088 r_scbond_other 4.087
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.43 r_dihedral_angle_3_deg 11.116 r_long_range_B_other 10.441 r_dihedral_angle_1_deg 7.546 r_scangle_other 6.266 r_dihedral_angle_2_deg 5.69 r_mcangle_it 5.661 r_mcangle_other 5.66 r_scbond_it 4.088 r_scbond_other 4.087 r_mcbond_it 3.634 r_mcbond_other 3.634 r_rigid_bond_restr 2.23 r_angle_refined_deg 1.374 r_angle_other_deg 0.511 r_chiral_restr 0.075 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 4654 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling REFMAC phasing PDB_EXTRACT data extraction