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Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103
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% w/v PEG 3350, 0.2 M di-Ammonium Citrate
Crystal Properties Matthews coefficient Solvent content 2.18 43.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.574 α = 90 b = 87.975 β = 96.94 c = 73.136 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 1.7 50 99.8 0.051 0.055 0.021 0.994 10 6.4 67209
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 1.7 1.73 99.1 0.981 1.071 0.424 0.716 6
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 1.7 48.26 63834 3333 99.45 0.1798 0.17842 0.1867 0.20634 0.2139 RANDOM 30.504
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] 0.38 -1.17 0.3 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.003 r_dihedral_angle_1_deg 7.592 r_dihedral_angle_2_deg 5.714 r_long_range_B_refined 5.11 r_long_range_B_other 5.043 r_scangle_other 2.798 r_mcangle_it 2.442 r_mcangle_other 2.441 r_scbond_it 1.732 r_scbond_other 1.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.003 r_dihedral_angle_1_deg 7.592 r_dihedral_angle_2_deg 5.714 r_long_range_B_refined 5.11 r_long_range_B_other 5.043 r_scangle_other 2.798 r_mcangle_it 2.442 r_mcangle_other 2.441 r_scbond_it 1.732 r_scbond_other 1.732 r_mcbond_it 1.477 r_mcbond_other 1.476 r_angle_refined_deg 1.328 r_angle_other_deg 0.48 r_chiral_restr 0.067 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4711 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction REFMAC phasing