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Human WRN helicase in complex with allosteric ligand Compound 1
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, HANGING DROP 277 23-24.5% w/v PEG1500, 100 mM MMT, pH 5.75-6.25
Crystal Properties Matthews coefficient Solvent content 2.39 48.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.141 α = 90 b = 58.215 β = 90 c = 133.287 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 100 PIXEL DECTRIS EIGER X 16M 2023-08-17 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 2.34 53.41 75.3 0.116 0.987 10.7 8.2 14840
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 2.342 2.522 53.3 0.558 1.4 9.1
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 2.34 53.41 13398 1442 75.26 0.25028 0.2445 0.2422 0.30114 0.2911 RANDOM 60.103
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] 0.4 -0.67 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.302 r_dihedral_angle_4_deg 17.926 r_dihedral_angle_3_deg 14.919 r_long_range_B_refined 7.618 r_long_range_B_other 7.617 r_dihedral_angle_1_deg 6.612 r_mcangle_it 5.356 r_mcangle_other 5.355 r_scangle_other 4.538 r_mcbond_it 3.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.302 r_dihedral_angle_4_deg 17.926 r_dihedral_angle_3_deg 14.919 r_long_range_B_refined 7.618 r_long_range_B_other 7.617 r_dihedral_angle_1_deg 6.612 r_mcangle_it 5.356 r_mcangle_other 5.355 r_scangle_other 4.538 r_mcbond_it 3.179 r_mcbond_other 3.177 r_scbond_it 2.639 r_scbond_other 2.638 r_angle_refined_deg 1.379 r_angle_other_deg 1.111 r_chiral_restr 0.052 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 3338 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 52
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction