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Crystal structure of WRN helicase with bound compound 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 24.5% w/v PEG1500, 0.1 M MMT, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.82 α = 90 b = 57.75 β = 90 c = 133.53 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER2 X CdTe 16M 2023-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.12 53.06 99.4 0.094 0.997 12.1 7.3 26085
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.15 0.564 6.6
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 2.12 53.06 24831 1252 99.36 0.22987 0.22801 0.2302 0.26659 0.2659 RANDOM 47.055
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] -1.21 0.93 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.952 r_dihedral_angle_4_deg 16.057 r_dihedral_angle_3_deg 13.644 r_dihedral_angle_1_deg 6.716 r_long_range_B_refined 5.106 r_long_range_B_other 5.1 r_mcangle_it 3.265 r_mcangle_other 3.265 r_scangle_other 2.84 r_mcbond_it 1.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.952 r_dihedral_angle_4_deg 16.057 r_dihedral_angle_3_deg 13.644 r_dihedral_angle_1_deg 6.716 r_long_range_B_refined 5.106 r_long_range_B_other 5.1 r_mcangle_it 3.265 r_mcangle_other 3.265 r_scangle_other 2.84 r_mcbond_it 1.951 r_mcbond_other 1.95 r_scbond_it 1.703 r_scbond_other 1.702 r_angle_refined_deg 1.348 r_angle_other_deg 1.118 r_chiral_restr 0.055 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 3368 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 49
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling XSCALE data scaling REFMAC refinement