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Human Exonuclease 5 crystal structure in complex with a ssDNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LW7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 16% PEG 3350 and 0.2 M lithium acetate
Crystal Properties Matthews coefficient Solvent content 2.44 49.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.17 α = 90 b = 83.98 β = 90 c = 96.355 γ = 90
Symmetry Space Group P 2 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 PILATUS3 6M 2019-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
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 2.88 48.18 100 0.436 0.455 0.126 0.986 6.4 12.8 9904
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 2.88 3.04 100 2.043 2.126 0.585 0.62 1.6 13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7LW7 2.88 48.178 1.35 9872 478 99.98 0.2073 0.2046 0.2035 0.2586 0.2588 39.7004
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.44 f_angle_d 0.481 f_chiral_restr 0.037 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms 184 Solvent Atoms 41 Heterogen Atoms 21
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction