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Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70
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 5.5 291 30% PEG3350 ,0.1M Ammonium Sulphate, 0.1M Bis-Tris pH5.5
Crystal Properties Matthews coefficient Solvent content 2.21 44.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.956 α = 90 b = 87.919 β = 98.72 c = 73.878 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 EIGER2 X 16M 2020-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.62 50 97.4 0.041 0.048 0.024 13.5 3.5 76489
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 1.62 1.65 78.4 0.516 0.651 0.39 0.666 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4PXW 1.62 44 72666 3744 97.32 0.2069 0.2056 0.2125 0.2335 0.2374 RANDOM 26.441
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] 0.83 -0.94 -0.24 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_dihedral_angle_4_deg 14.521 r_dihedral_angle_3_deg 11.823 r_dihedral_angle_1_deg 7.911 r_angle_refined_deg 1.307 r_angle_other_deg 1.283 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.478 r_dihedral_angle_4_deg 14.521 r_dihedral_angle_3_deg 11.823 r_dihedral_angle_1_deg 7.911 r_angle_refined_deg 1.307 r_angle_other_deg 1.283 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4608 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing