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Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 11
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 0.1M Tris pH 7.5, 2.18M Lithium acetate
Crystal Properties Matthews coefficient Solvent content 2.7 54.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.74 α = 90 b = 81.74 β = 90 c = 234.101 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 S 16M 2016-12-12 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) 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 2.09 234.1 100 0.999 14.3 19 28474
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.15 0.746
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.09 70.889 28381 1412 100 0.173 0.1713 0.2015 0.179 34.24
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] 0.215 0.108 0.215 -0.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_dihedral_angle_3_deg 16.265 r_dihedral_angle_4_deg 14.044 r_dihedral_angle_1_deg 8.724 r_lrange_it 7.322 r_lrange_other 7.103 r_scangle_it 4.315 r_scangle_other 4.065 r_mcangle_it 3.245 r_mcangle_other 3.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_dihedral_angle_3_deg 16.265 r_dihedral_angle_4_deg 14.044 r_dihedral_angle_1_deg 8.724 r_lrange_it 7.322 r_lrange_other 7.103 r_scangle_it 4.315 r_scangle_other 4.065 r_mcangle_it 3.245 r_mcangle_other 3.245 r_scbond_it 2.85 r_scbond_other 2.642 r_angle_refined_deg 2.211 r_mcbond_it 2.049 r_mcbond_other 2.039 r_angle_other_deg 1.459 r_chiral_restr 0.291 r_symmetry_nbd_other 0.191 r_nbd_refined 0.187 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.182 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2384 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing