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Crystal Structure of Human WRN helicase with compound 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other A previously solved structure of hWRN was used as a search model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 290 protocol was established using PROTEROS Standard Protocols
Crystal Properties Matthews coefficient Solvent content 2.32 47.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.293 α = 90 b = 58.216 β = 90 c = 131.619 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 100 PIXEL DECTRIS EIGER X 16M 2022-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.368 65.81 100 0.05 0.05 18 8.1 95235
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.368 1.392 100 1.308 1.308 1.3 7.5
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 1.37 65.81 86011 4433 94.93 0.2037 0.20313 0.2104 0.21414 0.2221 RANDOM 24.074
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] 0.37 -0.39 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.925 r_dihedral_angle_4_deg 13.89 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 5.608 r_long_range_B_refined 4.555 r_long_range_B_other 4.155 r_scangle_other 1.683 r_mcangle_it 1.562 r_mcangle_other 1.562 r_angle_refined_deg 1.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.925 r_dihedral_angle_4_deg 13.89 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 5.608 r_long_range_B_refined 4.555 r_long_range_B_other 4.155 r_scangle_other 1.683 r_mcangle_it 1.562 r_mcangle_other 1.562 r_angle_refined_deg 1.326 r_angle_other_deg 1.15 r_scbond_it 1.012 r_scbond_other 1.012 r_mcbond_it 0.895 r_mcbond_other 0.894 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3372 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 48
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data reduction autoPROC data scaling Aimless data scaling REFMAC refinement PHASER phasing PDB_EXTRACT data extraction