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Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (cmr)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 290 100 mM sodium acetate, pH 7.0; 10 mM KCl; 2-4% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.54 51.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.857 α = 90 b = 72.857 β = 90 c = 181.382 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 3.048 50 99.4 0.077 27.54 6.5 9928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.1 0.682
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 5V05 3.048 38.498 1.34 9870 797 99.36 0.2151 0.211 0.2166 0.2597 0.2649 124.7256
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 24.913 f_angle_d 0.853 f_chiral_restr 0.225 f_bond_d 0.004 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2734 Nucleic Acid Atoms 448 Solvent Atoms 100 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing