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Crystal structure of the WDR domain of WDR91 in complex with DR3634
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 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M of each alcohol,0.1M MES/imidazole pH6.5
Crystal Properties Matthews coefficient Solvent content 3.77 67.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.201 α = 90 b = 132.236 β = 90 c = 118.291 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 2024-10-08 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 0.071 0.076 0.027 0.999 12.5 7.9 27368
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 0.971 1.049 0.39 0.694 7
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 25.9 25931 1376 99.45 0.20171 0.1998 0.206 0.23777 0.237 RANDOM 49.79
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] -0.69 -0.57 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.715 r_dihedral_angle_2_deg 11.556 r_dihedral_angle_1_deg 8.406 r_long_range_B_other 7.657 r_long_range_B_refined 7.655 r_scangle_other 5.333 r_mcangle_it 4.372 r_mcangle_other 4.371 r_scbond_it 3.515 r_scbond_other 3.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.715 r_dihedral_angle_2_deg 11.556 r_dihedral_angle_1_deg 8.406 r_long_range_B_other 7.657 r_long_range_B_refined 7.655 r_scangle_other 5.333 r_mcangle_it 4.372 r_mcangle_other 4.371 r_scbond_it 3.515 r_scbond_other 3.513 r_mcbond_it 2.84 r_mcbond_other 2.839 r_angle_refined_deg 1.405 r_angle_other_deg 0.473 r_chiral_restr 0.067 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 2544 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction