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Crystal structure of WDR91 in complex with XS381295
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 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M of each divalent cation, 0.1M MES/imidazole pH6.5
Crystal Properties Matthews coefficient Solvent content 3.79 67.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.632 α = 90 b = 132.382 β = 90 c = 119.604 γ = 90
Symmetry Space Group C 2 2 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 CCD RIGAKU SATURN A200 2024-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 2.4 50 99.9 0.086 0.095 0.039 0.999 9.7 6 24659
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 2.4 2.44 100 0.966 1.059 0.43 0.716 6
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 2.4 27.7 23892 727 99.66 0.20042 0.19928 0.2041 0.23793 0.2379 RANDOM 44.17
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] 0.2 -0.24 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.278 r_dihedral_angle_2_deg 9.11 r_dihedral_angle_1_deg 8.508 r_long_range_B_other 6.296 r_long_range_B_refined 6.273 r_scangle_other 3.9 r_mcangle_it 3.548 r_mcangle_other 3.547 r_scbond_it 2.559 r_scbond_other 2.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.278 r_dihedral_angle_2_deg 9.11 r_dihedral_angle_1_deg 8.508 r_long_range_B_other 6.296 r_long_range_B_refined 6.273 r_scangle_other 3.9 r_mcangle_it 3.548 r_mcangle_other 3.547 r_scbond_it 2.559 r_scbond_other 2.558 r_mcbond_it 2.17 r_mcbond_other 2.168 r_angle_refined_deg 1.295 r_angle_other_deg 0.429 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2545 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing