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Crystal structure of Staphylococcal nuclease variant Delta+PHS V66E A109E at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC PDB ENTRY 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.145 α = 90 b = 54.159 β = 90 c = 108.125 γ = 90
Symmetry Space Group P 21 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 110 CCD APEX II CCD multi-layer optics 2013-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.54
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 1.67 50 99.8 0.0257 29.33 13.02 32967 32967 22.1
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 1.67 1.69 100 0.2281 4.37 5.57 1147
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 PDB ENTRY 3BDC 1.67 48.47 32906 32906 1669 99.97 0.1593 0.1593 0.1576 0.1695 0.1907 0.1994 RANDOM 14.816
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] 0.59 -0.09 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.511 r_dihedral_angle_4_deg 18.061 r_dihedral_angle_3_deg 14.146 r_dihedral_angle_1_deg 6.238 r_angle_refined_deg 1.798 r_mcangle_it 1.253 r_angle_other_deg 0.797 r_mcbond_it 0.779 r_mcbond_other 0.778 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.511 r_dihedral_angle_4_deg 18.061 r_dihedral_angle_3_deg 14.146 r_dihedral_angle_1_deg 6.238 r_angle_refined_deg 1.798 r_mcangle_it 1.253 r_angle_other_deg 0.797 r_mcbond_it 0.779 r_mcbond_other 0.778 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2157 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 52
Software Software Software Name Purpose SAINT data scaling SAINT data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data collection