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Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Staphyloccocal nuclease V66E/P117G/H124L/S128A variant (at 100K), with b-factors set to 20.0 A^2 and residue 66 truncated to Ala, waters excluded
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 37% MPD, 0.025 M potassium phosphate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.967 α = 90 b = 48.967 β = 90 c = 63.773 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 298 CCD APEX II CCD 2006-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER
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 2.1 50 99.4 0.0229 32.85 8.2 8881 8861
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) 2.1 2.2 100 0.1344 7.09 4.89 1141
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 Staphyloccocal nuclease V66E/P117G/H124L/S128A variant (at 100K), with b-factors set to 20.0 A^2 and residue 66 truncated to Ala, waters excluded 2.1 50 8810 8810 938 99.4 0.203 0.203 0.186 0.1857 0.23 0.2305 random 30.354
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] -2.945 -2.945 5.89
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.895 c_scbond_it 2.573 c_mcangle_it 2.142 c_mcbond_it 1.413
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1039 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction APEX data collection APEX data reduction CNS phasing