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Crystal structure of Staphylcoccal nuclease variant Delta+PHS A109E at cryogenic temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BDC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 25% MPD, 25mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.96 α = 90 b = 54.283 β = 90 c = 108.533 γ = 90
Symmetry Space Group P 21 21 21
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 2015-01-16 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 1.64 55 99.9 0.0273 30.12 15.09 34804 34804 21.2
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 1.64 1.66 98.6 0.2227 5.34 6.38
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 3bdc 1.64 54.27 33022 1723 99.87 0.1583 0.1567 0.1689 0.1897 0.2039 RANDOM 15.267
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] -0.13 -0.02 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_dihedral_angle_4_deg 15.999 r_dihedral_angle_3_deg 13.276 r_dihedral_angle_1_deg 6.267 r_angle_other_deg 1.854 r_angle_refined_deg 1.807 r_mcangle_it 1.647 r_mcbond_it 1.128 r_mcbond_other 1.117 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.598 r_dihedral_angle_4_deg 15.999 r_dihedral_angle_3_deg 13.276 r_dihedral_angle_1_deg 6.267 r_angle_other_deg 1.854 r_angle_refined_deg 1.807 r_mcangle_it 1.647 r_mcbond_it 1.128 r_mcbond_other 1.117 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.012 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2144 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 52
Software Software Software Name Purpose SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction