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Crystal Structure of Human WRN helicase with compound 26
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previously determined WRN structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277 co-crystallization additive 46 [Proplex-E2-B4+29% glycerol]
Crystal Properties Matthews coefficient Solvent content 2.92 57.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.29 α = 90 b = 71.26 β = 90 c = 120.62 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 EIGER2 S 9M 2022-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.58 46.08 99.8 0.11 0.044 0.999 19.3 13.2 19421
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.58 2.69 99.8 1.284 0.377 0.744
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 2.58 46.08 18463 891 99.63 0.23588 0.23351 0.2361 0.28568 0.2867 RANDOM 66.334
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] 0.21 0.88 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.101 r_dihedral_angle_3_deg 13.394 r_dihedral_angle_4_deg 11.722 r_dihedral_angle_1_deg 5.285 r_long_range_B_refined 4.698 r_long_range_B_other 4.685 r_mcangle_it 2.954 r_mcangle_other 2.953 r_scangle_other 2.475 r_mcbond_it 1.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.101 r_dihedral_angle_3_deg 13.394 r_dihedral_angle_4_deg 11.722 r_dihedral_angle_1_deg 5.285 r_long_range_B_refined 4.698 r_long_range_B_other 4.685 r_mcangle_it 2.954 r_mcangle_other 2.953 r_scangle_other 2.475 r_mcbond_it 1.661 r_mcbond_other 1.661 r_scbond_it 1.403 r_scbond_other 1.403 r_angle_refined_deg 1.195 r_angle_other_deg 1.142 r_chiral_restr 0.206 r_gen_planes_other 0.009 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_bond_other_d 0.003 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 3357 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction