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Crystal structure of Staphylococcal nuclease variant Delta+PHS V23D/T62H 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 21% MPD, 25 mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.194 α = 90 b = 60.236 β = 94.19 c = 38.49 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 2013-04-27 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 1.58 50 100 0.0204 29.76 11.83 19546 23.7
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 1.58 1.61 100 0.1682 5.57 7.99
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 1.58 31.11 18522 998 99.96 0.1596 0.1574 0.1683 0.1979 0.2 RANDOM 19.696
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 -0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_sphericity_free 15.155 r_dihedral_angle_3_deg 12.298 r_dihedral_angle_4_deg 10.737 r_rigid_bond_restr 7.77 r_sphericity_bonded 6.864 r_dihedral_angle_1_deg 6.402 r_angle_refined_deg 1.784 r_angle_other_deg 0.828 r_chiral_restr 0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.614 r_sphericity_free 15.155 r_dihedral_angle_3_deg 12.298 r_dihedral_angle_4_deg 10.737 r_rigid_bond_restr 7.77 r_sphericity_bonded 6.864 r_dihedral_angle_1_deg 6.402 r_angle_refined_deg 1.784 r_angle_other_deg 0.828 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1037 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 26
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Coot model building APEX data scaling APEX data reduction