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Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 13
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, SITTING DROP 7.5 293 1.91M LiSO4, 0.1M Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.12 60.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.577 α = 90 b = 81.577 β = 90 c = 234.132 γ = 120
Symmetry Space Group P 61 2 2
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 EIGER2 X 16M 2022-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
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 2.25 52.43 100 0.271 0.278 0.059 0.996 11.4 21.8 22902
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 2.25 2.32 100 2.748 2.81 0.583 0.771 22.9
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 2.25 52.43 21677 1141 99.96 0.1826 0.18052 0.1862 0.22018 0.2167 RANDOM 40.928
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] 0.69 0.34 0.69 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_4_deg 22.046 r_dihedral_angle_3_deg 16.154 r_dihedral_angle_1_deg 9.256 r_long_range_B_refined 6.821 r_long_range_B_other 6.813 r_scangle_other 4.641 r_mcangle_it 4.173 r_mcangle_other 4.158 r_scbond_it 3.034
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.262 r_dihedral_angle_4_deg 22.046 r_dihedral_angle_3_deg 16.154 r_dihedral_angle_1_deg 9.256 r_long_range_B_refined 6.821 r_long_range_B_other 6.813 r_scangle_other 4.641 r_mcangle_it 4.173 r_mcangle_other 4.158 r_scbond_it 3.034 r_scbond_other 3.033 r_mcbond_it 2.608 r_mcbond_other 2.587 r_angle_refined_deg 2.079 r_angle_other_deg 1.387 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 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 2367 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing