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Human WRN helicase in complex with allosteric ligand Compound 6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other proprietary model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20.0% w/v PEG3350, 200 mM ammonium tartrate
Crystal Properties Matthews coefficient Solvent content 2.27 45.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.085 α = 90.03 b = 58.394 β = 90 c = 131.907 γ = 90
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 EIGER2 X 16M 2023-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.556 53.5 94.4 0.036 0.998 11.4 2.3 234986
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.556 1.583 66.6 0.496 0.734 1.3 2.1
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 1.56 53.46 226751 8235 94.41 0.15124 0.1497 0.1603 0.19234 0.1972 RANDOM 31.791
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] 1.78 0.01 -0.03 0.45 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.246 r_dihedral_angle_4_deg 15.39 r_dihedral_angle_3_deg 12.189 r_dihedral_angle_1_deg 6.443 r_long_range_B_refined 4.028 r_long_range_B_other 3.806 r_scangle_other 2.986 r_mcangle_it 2.869 r_mcangle_other 2.869 r_rigid_bond_restr 2.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.246 r_dihedral_angle_4_deg 15.39 r_dihedral_angle_3_deg 12.189 r_dihedral_angle_1_deg 6.443 r_long_range_B_refined 4.028 r_long_range_B_other 3.806 r_scangle_other 2.986 r_mcangle_it 2.869 r_mcangle_other 2.869 r_rigid_bond_restr 2.443 r_scbond_it 2.381 r_scbond_other 2.381 r_mcbond_it 2.198 r_mcbond_other 2.196 r_angle_refined_deg 1.331 r_angle_other_deg 1.304 r_chiral_restr 0.066 r_bond_other_d 0.009 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13643 Nucleic Acid Atoms Solvent Atoms 1504 Heterogen Atoms 297
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling PDB_EXTRACT data extraction