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Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15
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 2.13M LiSO4, 0.1M Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.67 53.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.496 α = 90 b = 81.496 β = 90 c = 232.723 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 PILATUS3 6M 2017-05-01 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 1.497 52.259 99.6 0.091 0.097 0.033 0.997 11.1 8.7 74179
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 1.5 1.52 94 1.726 1.852 0.652 0.452 7.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.497 52.259 74110 3672 99.557 0.171 0.17 0.1697 0.186 0.1857 20.866
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] 0.224 0.112 0.224 -0.728
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 13.465 r_dihedral_angle_1_deg 7.982 r_lrange_it 6.884 r_lrange_other 6.712 r_scangle_it 3.787 r_scangle_other 3.605 r_scbond_it 2.563 r_angle_refined_deg 2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_dihedral_angle_4_deg 18.377 r_dihedral_angle_3_deg 13.465 r_dihedral_angle_1_deg 7.982 r_lrange_it 6.884 r_lrange_other 6.712 r_scangle_it 3.787 r_scangle_other 3.605 r_scbond_it 2.563 r_angle_refined_deg 2.5 r_scbond_other 2.44 r_mcangle_other 2.409 r_mcangle_it 2.407 r_angle_other_deg 1.615 r_mcbond_it 1.487 r_mcbond_other 1.464 r_chiral_restr 0.365 r_xyhbond_nbd_refined 0.207 r_symmetry_xyhbond_nbd_refined 0.207 r_nbd_refined 0.203 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.175 r_nbd_other 0.172 r_symmetry_xyhbond_nbd_other 0.15 r_symmetry_nbtor_other 0.09 r_metal_ion_refined 0.068 r_bond_refined_d 0.021 r_gen_planes_refined 0.015 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2384 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing