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Crystal structure of apo WRN helicase in Form D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9MJS
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 2.18 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.746 α = 90 b = 58.208 β = 90 c = 130.666 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 2022-05-11 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 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 1.73 65.33 100 0.078 0.996 13.3 8.2 46791
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 1.73 1.76 0.59 1.3 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 1.73 65.33 43948 2843 99.95 0.21975 0.21724 0.2215 0.25888 0.2658 RANDOM 38.082
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] 0.23 1.01 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.035 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_4_deg 10.577 r_dihedral_angle_1_deg 6.826 r_long_range_B_refined 5.076 r_long_range_B_other 5.034 r_scangle_other 3.146 r_mcangle_it 2.97 r_mcangle_other 2.97 r_scbond_it 1.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.035 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_4_deg 10.577 r_dihedral_angle_1_deg 6.826 r_long_range_B_refined 5.076 r_long_range_B_other 5.034 r_scangle_other 3.146 r_mcangle_it 2.97 r_mcangle_other 2.97 r_scbond_it 1.924 r_scbond_other 1.923 r_mcbond_it 1.837 r_mcbond_other 1.835 r_angle_refined_deg 1.327 r_angle_other_deg 1.174 r_chiral_restr 0.061 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 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 3396 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling