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Crystal structure of the WDR domain of WDR91 in complex with DR3460
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 291 12.5%(w/v) PEG 4K, 20%(v/v) 1,2,6-hexanetriol 0.02 M of each Monosaccharide II 0.1 M MOPSO/bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.82 67.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.834 α = 90 b = 132.976 β = 90 c = 119.62 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 2024-07-09 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 2.31 50 99.9 0.058 0.062 0.022 1 11.6 8 27927
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 2.31 2.35 100 0.981 1.049 0.369 0.773 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 (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 2.31 25.84 26469 1412 99.76 0.19993 0.19768 0.204 0.24249 0.2418 RANDOM 49.874
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] 0.01 -1.07 1.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.01 r_dihedral_angle_2_deg 12.525 r_dihedral_angle_1_deg 8.171 r_long_range_B_refined 7.229 r_long_range_B_other 7.227 r_scangle_other 4.859 r_mcangle_it 3.703 r_mcangle_other 3.703 r_scbond_it 3.18 r_scbond_other 3.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.01 r_dihedral_angle_2_deg 12.525 r_dihedral_angle_1_deg 8.171 r_long_range_B_refined 7.229 r_long_range_B_other 7.227 r_scangle_other 4.859 r_mcangle_it 3.703 r_mcangle_other 3.703 r_scbond_it 3.18 r_scbond_other 3.178 r_mcbond_it 2.438 r_mcbond_other 2.435 r_angle_refined_deg 1.225 r_angle_other_deg 0.429 r_chiral_restr 0.061 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 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 2542 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