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Crystal structure of WRN in complex with (S)-27 (GSK5819992)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 7% PEG 20000, 0.1 M MES pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.41 α = 90 b = 57.933 β = 91.31 c = 133.241 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2024-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9655 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 133.21 95.1 0.072 0.087 0.037 0.999 14.7 5.6 49800
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 1.374 1.559 0.653 0.59 1.8 5.7
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 2.1 58.39 47299 2385 88.99 0.19958 0.19702 0.2019 0.24943 0.2517 RANDOM 43.644
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] 3.53 0.5 -1.96 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.524 r_dihedral_angle_2_deg 13.379 r_long_range_B_refined 8.77 r_long_range_B_other 8.767 r_dihedral_angle_1_deg 8.389 r_scangle_other 6.327 r_mcangle_it 5.653 r_mcangle_other 5.653 r_scbond_it 4.369 r_scbond_other 4.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.524 r_dihedral_angle_2_deg 13.379 r_long_range_B_refined 8.77 r_long_range_B_other 8.767 r_dihedral_angle_1_deg 8.389 r_scangle_other 6.327 r_mcangle_it 5.653 r_mcangle_other 5.653 r_scbond_it 4.369 r_scbond_other 4.369 r_mcbond_it 3.92 r_mcbond_other 3.92 r_angle_refined_deg 1.235 r_angle_other_deg 0.409 r_chiral_restr 0.064 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 6796 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing