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Crystal structure of WRN helicase with bound allosteric compound 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 PEG1500, 0.1 M MMT, pH 5.75-6.25
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.13 α = 90 b = 58.067 β = 90 c = 131.561 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 XE 16M 2023-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95372 Diamond I04
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 1.7 34.87 100 0.037 0.996 22.6 8.3 49994
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 1.7 1.73 0.699 1.4 8.2
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 1.7 34.87 41609 893 84.98 0.21054 0.20945 0.2141 0.26144 0.2622 RANDOM 40.812
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] 0.95 -0.27 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.794 r_dihedral_angle_4_deg 18.356 r_dihedral_angle_3_deg 12.397 r_dihedral_angle_1_deg 6.936 r_long_range_B_refined 5.583 r_long_range_B_other 5.569 r_rigid_bond_restr 4.905 r_scangle_other 3.808 r_mcangle_it 3.491 r_mcangle_other 3.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.794 r_dihedral_angle_4_deg 18.356 r_dihedral_angle_3_deg 12.397 r_dihedral_angle_1_deg 6.936 r_long_range_B_refined 5.583 r_long_range_B_other 5.569 r_rigid_bond_restr 4.905 r_scangle_other 3.808 r_mcangle_it 3.491 r_mcangle_other 3.491 r_scbond_it 2.542 r_scbond_other 2.541 r_mcbond_it 2.452 r_mcbond_other 2.452 r_angle_refined_deg 1.426 r_angle_other_deg 1.235 r_chiral_restr 0.069 r_bond_refined_d 0.006 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3366 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 72
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement