☰ Navigation Tabs
Crystal structure of Staphylcoccal nuclease variant Delta+PHS I72K/V74K at pH 9.0 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 9 277 20% MPD, 25mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.809 α = 90 b = 60.204 β = 90 c = 73.827 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 2014-04-28 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 0.0237 33.96 18.49 19443 19443 19.7
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 1.6 1.62 100 0.1827 5.09 5.73
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 1.6 31.47 19388 991 99.97 0.1713 0.17 0.182 0.1947 0.205 RANDOM 13.591
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] -0.07 0.22 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_3_deg 15.325 r_dihedral_angle_4_deg 13.299 r_dihedral_angle_1_deg 6.879 r_angle_refined_deg 1.863 r_angle_other_deg 1.131 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.975 r_dihedral_angle_3_deg 15.325 r_dihedral_angle_4_deg 13.299 r_dihedral_angle_1_deg 6.879 r_angle_refined_deg 1.863 r_angle_other_deg 1.131 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1053 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 26
Software Software Software Name Purpose SAINT data reduction PDB_EXTRACT data extraction PHASER phasing REFMAC refinement