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Crystal structure of the WDR domain of WDR91 in complex with DR3448
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 8K, 20%(v/v) 1,5-pentanediol 0.02 M of each Amino-acid II 0.1 M MOPSO/bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.87 57.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.428 α = 119.12 b = 76.316 β = 95.9 c = 77.043 γ = 102.57
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 2.1 50 95 0.061 0.068 0.03 0.999 14.8 5 50289
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 2.1 2.14 84.1 0.699 0.796 0.375 0.731 4
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 2.1 28.05 48873 1369 94.53 0.1889 0.18772 0.1952 0.23279 0.2389 RANDOM 51.488
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] -1.75 0.62 0.73 0.45 0.9 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.9 r_dihedral_angle_2_deg 11.716 r_dihedral_angle_1_deg 8.429 r_long_range_B_refined 6.827 r_long_range_B_other 6.817 r_scangle_other 4.782 r_mcangle_other 4.23 r_mcangle_it 4.229 r_scbond_it 3.256 r_scbond_other 3.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.9 r_dihedral_angle_2_deg 11.716 r_dihedral_angle_1_deg 8.429 r_long_range_B_refined 6.827 r_long_range_B_other 6.817 r_scangle_other 4.782 r_mcangle_other 4.23 r_mcangle_it 4.229 r_scbond_it 3.256 r_scbond_other 3.256 r_mcbond_it 2.939 r_mcbond_other 2.939 r_angle_refined_deg 1.258 r_angle_other_deg 0.446 r_chiral_restr 0.065 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 5046 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PHASER phasing HKL-3000 data reduction