☰ Navigation Tabs
Crystal structure of minor pseudopilin ternary complex of XcpVWX from the Type 2 secretion system of Pseudomonas aeruginosa in the P3 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 19 %-22 % PEG 2000 MME, 0.1 M Tris, pH 8.0-9.0, 0.2 M trimethylamine N-oxide (TMAO)
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.1 α = 90 b = 158.1 β = 90 c = 64.7 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 100 PIXEL DECTRIS PILATUS3 X 1M 2017-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.83 19.91 99.2 0.998 12.77 10 42465 79.02
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.83 3 0.646
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5VTM 2.85 19.91 1.94 42152 2108 100 0.2183 0.2143 0.2154 0.2941 0.2926 73.29
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 18.4758 f_angle_d 1.1021 f_chiral_restr 0.054 f_bond_d 0.009 f_plane_restr 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10549 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction XDS data scaling PHENIX model building PHASER phasing