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Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 6
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, 1.66M Lithium acetate
Crystal Properties Matthews coefficient Solvent content 3.13 60.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.581 α = 90 b = 81.581 β = 90 c = 234.805 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 2022-09-24 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 2.2 46.96 100 0.995 16 29.5 24491
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 2.2 2.27 0.703
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 2.2 45.191 24406 1237 99.984 0.187 0.1853 0.1837 0.2086 0.208 59.031
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] 0.24 0.12 0.24 -0.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.512 r_dihedral_angle_4_deg 24.574 r_dihedral_angle_3_deg 17.288 r_dihedral_angle_1_deg 8.565 r_lrange_it 8.344 r_lrange_other 8.215 r_scangle_it 6.135 r_scangle_other 5.943 r_mcangle_other 4.695 r_mcangle_it 4.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.512 r_dihedral_angle_4_deg 24.574 r_dihedral_angle_3_deg 17.288 r_dihedral_angle_1_deg 8.565 r_lrange_it 8.344 r_lrange_other 8.215 r_scangle_it 6.135 r_scangle_other 5.943 r_mcangle_other 4.695 r_mcangle_it 4.691 r_scbond_it 4.26 r_scbond_other 4.068 r_mcbond_it 3.095 r_mcbond_other 3.085 r_angle_refined_deg 1.988 r_angle_other_deg 1.437 r_nbd_other 0.231 r_symmetry_nbd_other 0.198 r_nbd_refined 0.197 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.12 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2363 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing