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Co-crystal structure of the WD-repeat domain of human WDR91 in complex with MR46654
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 12% (w/v) PEG3350, 0.2 M KCl, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.696 α = 90 b = 121.618 β = 90 c = 132.027 γ = 90
Symmetry Space Group P 21 21 21
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 2023-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2.2 50 97.9 0.08 0.086 0.032 0.998 6.2 7.7 62021
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 2.2 2.24 98.4 1.014 1.083 0.375 0.826 8.2
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 2.2 38.78 60770 1207 97.77 0.2455 0.24466 0.2504 0.28777 0.2923 RANDOM 57.441
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] -1.21 0.78 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.999 r_dihedral_angle_4_deg 18.873 r_dihedral_angle_3_deg 15.187 r_dihedral_angle_1_deg 8.408 r_long_range_B_refined 5.093 r_long_range_B_other 5.076 r_scangle_other 2.282 r_mcangle_it 2.049 r_mcangle_other 2.048 r_scbond_it 1.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.999 r_dihedral_angle_4_deg 18.873 r_dihedral_angle_3_deg 15.187 r_dihedral_angle_1_deg 8.408 r_long_range_B_refined 5.093 r_long_range_B_other 5.076 r_scangle_other 2.282 r_mcangle_it 2.049 r_mcangle_other 2.048 r_scbond_it 1.413 r_scbond_other 1.413 r_angle_refined_deg 1.27 r_mcbond_it 1.223 r_mcbond_other 1.223 r_angle_other_deg 1.179 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 7238 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction