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Crystal structure of WDR91 in complex with XS838489
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 7.5 291 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M of each alcohol, 0.1M MOPS/HEPES-Na pH7.5
Crystal Properties Matthews coefficient Solvent content 3.75 67.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.613 α = 90 b = 132.547 β = 90 c = 119.797 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 PIXEL DECTRIS PILATUS3 2M 2024-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
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 2.22 50 100 0.062 0.065 0.019 1 9.7 10.8 30949
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 2.22 2.26 100 0.904 0.949 0.286 0.802 10.8
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 2.22 44.69 29329 1573 99.77 0.2047 0.20262 0.2065 0.24497 0.2466 RANDOM 44.285
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] 1.19 -0.93 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.382 r_long_range_B_other 8.506 r_long_range_B_refined 8.498 r_dihedral_angle_2_deg 7.567 r_dihedral_angle_1_deg 7.494 r_scangle_other 6.006 r_mcangle_it 5.486 r_mcangle_other 5.485 r_scbond_it 3.88 r_scbond_other 3.879
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.382 r_long_range_B_other 8.506 r_long_range_B_refined 8.498 r_dihedral_angle_2_deg 7.567 r_dihedral_angle_1_deg 7.494 r_scangle_other 6.006 r_mcangle_it 5.486 r_mcangle_other 5.485 r_scbond_it 3.88 r_scbond_other 3.879 r_mcbond_it 3.578 r_mcbond_other 3.572 r_angle_refined_deg 1.342 r_angle_other_deg 0.471 r_chiral_restr 0.064 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 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 2535 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASES phasing