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Crystal structure of Staphylococcal nuclease variant Delta+PHS K64G/V66K/E67G 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 25% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.831 α = 90 b = 60.549 β = 93.15 c = 77.901 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 multi-layer optics 2014-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
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 50 100 0.0261 29.29 18.84 26668 26668 25.2
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 1.84 100 0.2336 4.24 7.33
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 1.8 50 25309 1319 99.91 0.1869 0.1849 0.2253 0.2222 RANDOM 21.809
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] 0.09 -0.07 0.04 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_4_deg 11.707 r_dihedral_angle_1_deg 5.984 r_mcangle_it 1.992 r_angle_refined_deg 1.792 r_mcbond_it 1.398 r_mcbond_other 1.383 r_angle_other_deg 0.838 r_chiral_restr 0.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_3_deg 16.301 r_dihedral_angle_4_deg 11.707 r_dihedral_angle_1_deg 5.984 r_mcangle_it 1.992 r_angle_refined_deg 1.792 r_mcbond_it 1.398 r_mcbond_other 1.383 r_angle_other_deg 0.838 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2024 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 52
Software Software Software Name Purpose APEX data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction APEX data reduction