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Crystal structure of Staphylococcal nuclease variant PHS T62K at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EY8 1EY8.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.22 α = 90 b = 48.22 β = 90 c = 63.28 γ = 90
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 BRUKER APEX II multi-layer optics 2005-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 17.98 99.8 0.0301 0.0199 30.16 10.6 14741 14710 33.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.84 99.3 0.2839 0.2574 4.05 3.43 2016
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1EY8.PDB 1.8 17 13483 12753 1272 94.61 0.23 0.203 0.198 0.199 0.255 0.251 RANDOM 27.909
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 r_dihedral_angle_2_deg 29.248 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 18.093 r_dihedral_angle_1_deg 7.47 r_scangle_it 7.239 r_scbond_it 5.07 r_mcangle_it 3.159 r_angle_refined_deg 2.08 r_mcbond_it 2.056 r_chiral_restr 0.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.248 r_dihedral_angle_4_deg 20.903 r_dihedral_angle_3_deg 18.093 r_dihedral_angle_1_deg 7.47 r_scangle_it 7.239 r_scbond_it 5.07 r_mcangle_it 3.159 r_angle_refined_deg 2.08 r_mcbond_it 2.056 r_chiral_restr 0.157 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1024 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 5
Software Software Software Name Purpose SAINT data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection SAINT data reduction