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Crystal structure of apo-NP exonuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 38% v/v Polyethylene glycol 200, 10 mM Aurintricarboxylic acid
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.129 α = 90 b = 121.276 β = 90 c = 137.722 γ = 90
Symmetry Space Group I 2 2 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 2015-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.97622 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 30 98.8 0.101 0.113 0.05 7.5 4.6 24007 35.59
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 2.4 2.49 98.3 0.494 0.574 0.285 0.723 3.7
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 4G9Z 2.403 28.739 1.37 23991 1873 97.6 0.2109 0.2079 0.2097 0.248 0.2468 43.9128
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3163 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction