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Crystal structure of Staphylococcal nuclease variant Delta+PHS V66H/I72E 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 9 277 20% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.205 α = 90 b = 60.54 β = 93.56 c = 38.356 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 APEX II CCD mirrors 2015-01-28 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 1.7 60 100 0.0208 32.11 13.23 15763 24.4
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 1.7 1.73 100 0.1307 6.19 7.44
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 1.7 38.28 14881 804 99.61 0.1997 0.1976 0.2061 0.237 0.2446 RANDOM 20.625
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] -0.03 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_3_deg 14.964 r_dihedral_angle_1_deg 7.076 r_dihedral_angle_4_deg 6.963 r_mcangle_it 2.858 r_mcbond_it 1.924 r_mcbond_other 1.891 r_angle_refined_deg 1.725 r_angle_other_deg 0.851 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.597 r_dihedral_angle_3_deg 14.964 r_dihedral_angle_1_deg 7.076 r_dihedral_angle_4_deg 6.963 r_mcangle_it 2.858 r_mcbond_it 1.924 r_mcbond_other 1.891 r_angle_refined_deg 1.725 r_angle_other_deg 0.851 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1046 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 26
Software Software Software Name Purpose XPREP data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX 2 data reduction