☰ Navigation Tabs
Crystal structure of Staphylcoccal nuclease variant Delta+PHS I92S 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 8 277 25% MPD, 25mM potassium phosphate, calcium chloride, pdTp
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.031 α = 90 b = 59.964 β = 93.63 c = 38.017 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 mirrors 2013-05-07 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 1.8 59.96 99.9 0.0347 18.95 9.08 12978 12978 27.2
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 1.83 100 0.2266 5.68
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 1.8 37.94 12950 630 99.81 0.1979 0.1964 0.2042 0.2269 0.231 RANDOM 22.129
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 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.432 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_4_deg 7.998 r_dihedral_angle_1_deg 6.486 r_angle_refined_deg 1.823 r_angle_other_deg 0.806 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.432 r_dihedral_angle_3_deg 15.243 r_dihedral_angle_4_deg 7.998 r_dihedral_angle_1_deg 6.486 r_angle_refined_deg 1.823 r_angle_other_deg 0.806 r_chiral_restr 0.116 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1031 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 26
Software Software Software Name Purpose SAINT data reduction SAINT data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction