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Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound
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 30% PEG2000 Monoethyl Ether, 0.2 M Potassium Bromide
Crystal Properties Matthews coefficient Solvent content 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.442 α = 90 b = 87.884 β = 96.75 c = 73.075 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 2M 2023-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 1.43 50 97.3 0.045 0.049 0.019 0.999 8.9 6.6 108966
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 1.43 1.45 81.7 0.463 0.511 0.21 0.898 5.5
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 1.43 42.5 103543 5396 97.14 0.14194 0.1405 0.153 0.16957 0.1752 RANDOM 16.638
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] 1.86 -0.53 -1.11 -0.61
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.071 r_dihedral_angle_3_deg 11.062 r_long_range_B_other 10.078 r_dihedral_angle_1_deg 7.547 r_scangle_other 5.932 r_dihedral_angle_2_deg 5.77 r_mcangle_other 5.32 r_mcangle_it 5.319 r_scbond_it 3.855 r_scbond_other 3.854
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.071 r_dihedral_angle_3_deg 11.062 r_long_range_B_other 10.078 r_dihedral_angle_1_deg 7.547 r_scangle_other 5.932 r_dihedral_angle_2_deg 5.77 r_mcangle_other 5.32 r_mcangle_it 5.319 r_scbond_it 3.855 r_scbond_other 3.854 r_mcbond_it 3.349 r_mcbond_other 3.343 r_rigid_bond_restr 2.085 r_angle_refined_deg 1.348 r_angle_other_deg 0.506 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 4698 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data processing HKL-3000 data reduction