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Crystal structure of Staphylococcal nuclease variant Delta+PHS T62E/V66K 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 28% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 1.97 37.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.858 α = 90 b = 60.412 β = 98.6 c = 34.568 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 2016-01-13 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 1.6 50 100 0.014 64.39 10 16640 22.4
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 1.6 1.66 100 0.098 8.96 7.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3BDC 1.6 34.18 15743 879 99.98 0.1821 0.18 0.221 0.2199 RANDOM 17.298
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.194 r_dihedral_angle_3_deg 16.049 r_dihedral_angle_4_deg 10.156 r_dihedral_angle_1_deg 5.509 r_mcangle_it 2.45 r_angle_refined_deg 1.775 r_mcbond_it 1.629 r_mcbond_other 1.629 r_angle_other_deg 0.875 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.194 r_dihedral_angle_3_deg 16.049 r_dihedral_angle_4_deg 10.156 r_dihedral_angle_1_deg 5.509 r_mcangle_it 2.45 r_angle_refined_deg 1.775 r_mcbond_it 1.629 r_mcbond_other 1.629 r_angle_other_deg 0.875 r_chiral_restr 0.116 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1063 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement CrysalisPro data scaling PHASER phasing PDB_EXTRACT data extraction CrysalisPro data reduction Coot model building