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SeMet crystal structure of the Neisseria meningitidis non-core minor pilin PilV in the monoclinic form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5V23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 100 mM Sodium Acetate pH 5,
100 mM ammonium chloride,
28 % w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.75 33.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.32 α = 90 b = 21.8 β = 104.24 c = 83.83 γ = 90
Symmetry Space Group C 1 2 1
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 2017-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.96859 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.407 40.63 95.9 0.098 0.043 0.997 12.2 5.9 15424
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.43 97 0.819 0.359 0.843 4 6 772
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 5V23 1.407 27.084 1.33 15402 811 95.19 0.1741 0.1722 0.1746 0.2064 0.2076
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 13.138 f_angle_d 1.024 f_chiral_restr 0.08 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 773 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing