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Crystal structure of Staphylococcal nuclease variant Delta+PHS T62K/V66E pH 7 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 7 277 30% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.21 44.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.062 α = 90 b = 60.498 β = 94.28 c = 38.3 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 mirrors 2015-08-13 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 1.85 50 100 0.02 50.97 10.1 12150 24.41
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 1.85 1.92 100 0.105 8.03 6.7
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 1.85 38.19 11469 665 99.93 0.1797 0.1774 0.1855 0.22 0.229 RANDOM 19.315
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] -0.02 0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_3_deg 15.49 r_dihedral_angle_4_deg 10.594 r_dihedral_angle_1_deg 6.062 r_mcangle_it 2.318 r_angle_refined_deg 1.854 r_mcbond_it 1.568 r_mcbond_other 1.546 r_angle_other_deg 0.951 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_3_deg 15.49 r_dihedral_angle_4_deg 10.594 r_dihedral_angle_1_deg 6.062 r_mcangle_it 2.318 r_angle_refined_deg 1.854 r_mcbond_it 1.568 r_mcbond_other 1.546 r_angle_other_deg 0.951 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 26
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrysalisPro data reduction CrysalisPro data scaling CrysalisPro data collection