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Crystal structure of WRN helicase with bound AMPPNP
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 6 277 30% Jeffamine ED 2003, 0.2 M NaCl, 0.2 M NDSB-201, 0.1 M MES
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.202 α = 90 b = 93.737 β = 104.44 c = 53.782 γ = 90
Symmetry Space Group C 1 2 1
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 2022-03-15 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 1.84 45.41 96.3 0.08 0.997 8.2 2.8 41646
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 1.84 1.87 96.2 0.528 2.9
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 1.84 45.41 39208 2413 96.17 0.19157 0.18946 0.1962 0.22518 0.228 RANDOM 32.904
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] 2.34 0.17 -1.81 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.696 r_dihedral_angle_4_deg 18.316 r_dihedral_angle_3_deg 12.52 r_dihedral_angle_1_deg 6.763 r_long_range_B_refined 5.207 r_long_range_B_other 5.156 r_scangle_other 3.575 r_mcangle_it 2.858 r_mcangle_other 2.858 r_scbond_it 2.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.696 r_dihedral_angle_4_deg 18.316 r_dihedral_angle_3_deg 12.52 r_dihedral_angle_1_deg 6.763 r_long_range_B_refined 5.207 r_long_range_B_other 5.156 r_scangle_other 3.575 r_mcangle_it 2.858 r_mcangle_other 2.858 r_scbond_it 2.258 r_scbond_other 2.258 r_mcbond_it 1.867 r_mcbond_other 1.862 r_angle_refined_deg 1.38 r_angle_other_deg 1.217 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 3239 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 32
Software Software Software Name Purpose autoPROC data reduction XDS data reduction autoPROC data scaling Aimless data scaling REFMAC refinement