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Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110
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 5.5 291 25% w/v PEG 3350, 0.1 M Ammonium Sulphate, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.858 α = 90 b = 87.712 β = 98.43 c = 73.828 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 S 6M 2024-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18049 CLSI 08B1-1
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 1.74 50 99.8 0.047 0.051 0.02 0.998 8.9 6.6 63218
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 1.74 1.77 99.7 0.903 0.987 0.394 0.703 6.1
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 MOLECULAR REPLACEMENT THROUGHOUT 1.74 48.38 60028 3163 99.57 0.18746 0.18555 0.1929 0.22444 0.2284 RANDOM 28.619
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] 0.97 -0.86 -0.05 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.895 r_dihedral_angle_2_deg 10.182 r_dihedral_angle_1_deg 7.991 r_long_range_B_refined 6.947 r_long_range_B_other 6.924 r_scangle_other 5.239 r_mcangle_other 4.111 r_mcangle_it 4.11 r_scbond_it 3.378 r_scbond_other 3.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.895 r_dihedral_angle_2_deg 10.182 r_dihedral_angle_1_deg 7.991 r_long_range_B_refined 6.947 r_long_range_B_other 6.924 r_scangle_other 5.239 r_mcangle_other 4.111 r_mcangle_it 4.11 r_scbond_it 3.378 r_scbond_other 3.377 r_mcbond_it 2.824 r_mcbond_other 2.823 r_angle_refined_deg 1.285 r_angle_other_deg 0.442 r_chiral_restr 0.064 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 4634 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling REFMAC phasing PDB_EXTRACT data extraction HKL-3000 data reduction