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Crystal structure of minor pilin TcpB from Vibrio cholerae complexed with secreted protein TcpF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7W63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 273 0.4 M trisodium citrate, 4%(w/v) PEG3350, 10%(w/v) xylitol.
Crystal Properties Matthews coefficient Solvent content 7.28 83.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 284.139 α = 90 b = 284.139 β = 90 c = 297.599 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS 6M 2019-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 4.05 49.21 99.9 0.17 0.175 0.04 0.999 13.1 19 57983
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.05 4.16 100 3.072 3.153 0.707 0.533 19.7
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 7W63 4.05 31.83 1.33 57800 5702 99.91 0.2768 0.2742 0.2762 0.3008 0.3038 221.44
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 14.1225 f_angle_d 0.7369 f_chiral_restr 0.0459 f_plane_restr 0.0042 f_bond_d 0.0039
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16441 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing