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Crystal structure of Staphylococcal nuclease variant Delta+PHS V23E/V66H 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 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.1 α = 90 b = 60.592 β = 93.97 c = 38.547 γ = 90
Symmetry Space Group P 1 21 1
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 AGILENT ATLAS CCD 2015-09-22 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 1.8 50 99.9 0.019 51.09 10.1 13318 25.8
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 1.8 1.87 100 0.123 6.24 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3BDC 1.8 38.45 12648 654 99.95 0.1912 0.1893 0.1973 0.2253 0.2295 RANDOM 21.929
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.827 r_dihedral_angle_3_deg 15.625 r_dihedral_angle_4_deg 10.621 r_dihedral_angle_1_deg 6.47 r_mcangle_it 2.824 r_mcbond_it 1.996 r_mcbond_other 1.976 r_angle_refined_deg 1.835 r_angle_other_deg 0.959 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.827 r_dihedral_angle_3_deg 15.625 r_dihedral_angle_4_deg 10.621 r_dihedral_angle_1_deg 6.47 r_mcangle_it 2.824 r_mcbond_it 1.996 r_mcbond_other 1.976 r_angle_refined_deg 1.835 r_angle_other_deg 0.959 r_chiral_restr 0.108 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1038 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 26
Software Software Software Name Purpose XPREP data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction