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Crystal structure of WRN helicase with bound allosteric fragment 3.
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 21%-27.5% (w/v) PEG 1500 and 0.1 M MMT pH 5.75-6.25
Crystal Properties Matthews coefficient Solvent content 2.32 46.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.599 α = 90 b = 62.299 β = 90 c = 135.107 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 S 16M 2022-11-19 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) 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 51.47 66.8 0.995 9.8 3.8 21778
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 2.03 0.511
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 51.47 21252 504 66.72 0.2218 0.22077 0.2252 0.26336 0.2635 RANDOM 38.426
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] 0.8 -0.57 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.446 r_dihedral_angle_4_deg 15.793 r_dihedral_angle_3_deg 15.527 r_dihedral_angle_1_deg 7.564 r_long_range_B_refined 3.466 r_long_range_B_other 3.425 r_mcangle_it 1.657 r_mcangle_other 1.656 r_angle_refined_deg 1.546 r_scangle_other 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.446 r_dihedral_angle_4_deg 15.793 r_dihedral_angle_3_deg 15.527 r_dihedral_angle_1_deg 7.564 r_long_range_B_refined 3.466 r_long_range_B_other 3.425 r_mcangle_it 1.657 r_mcangle_other 1.656 r_angle_refined_deg 1.546 r_scangle_other 1.43 r_angle_other_deg 1.197 r_mcbond_other 0.961 r_mcbond_it 0.96 r_scbond_it 0.862 r_scbond_other 0.861 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 3268 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 16
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement