☰ Navigation Tabs
Crystal structure of PA0091 VgrG1, the central spike of the Type VI Secretion System
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P5Z PDB Entry 2P5Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.4 M Li2SO4, 5% MPD, 100 mM BisTris, 10 mM CsCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 6.17 80.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.275 α = 90 b = 168.275 β = 90 c = 652.849 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 PIXEL PSI PILATUS 6M 2012-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 3.32 50 99.8 0.169 13.3 10.5 304602 304594 -3 70.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.32 3.5 99.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB Entry 2P5Z 3.322 49.143 1.99 304594 304249 6084 99.83 0.1825 0.1754 0.1697 0.1747 0.1954 0.1981 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.748 f_angle_d 1.003 f_chiral_restr 0.04 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29862 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 1302
Software Software Software Name Purpose RESOLVE model building PHENIX refinement XDS data reduction XDS data scaling RESOLVE phasing