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Crystal structure of WRN helicase with bound allosteric fragment 4
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 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.44 α = 90 b = 58.061 β = 90 c = 130.759 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 1.00 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 43.5 100 0.072 0.999 13.1 7.1 46408
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 0.495 1.3
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 43.45 45762 641 99.96 0.1995 0.19907 0.204 0.22933 0.2324 RANDOM 43.147
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] -1.13 1.92 -0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.507 r_dihedral_angle_4_deg 18.252 r_dihedral_angle_3_deg 13.478 r_dihedral_angle_1_deg 6.775 r_long_range_B_refined 5.824 r_long_range_B_other 5.803 r_scangle_other 1.647 r_mcangle_it 1.612 r_mcangle_other 1.611 r_angle_refined_deg 1.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.507 r_dihedral_angle_4_deg 18.252 r_dihedral_angle_3_deg 13.478 r_dihedral_angle_1_deg 6.775 r_long_range_B_refined 5.824 r_long_range_B_other 5.803 r_scangle_other 1.647 r_mcangle_it 1.612 r_mcangle_other 1.611 r_angle_refined_deg 1.414 r_angle_other_deg 1.295 r_scbond_it 1.011 r_scbond_other 1.011 r_mcbond_it 0.939 r_mcbond_other 0.935 r_chiral_restr 0.068 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 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 3416 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 61
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement