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Structure of VapBC from Shigella sonnei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 0.1 M Ammonium sulphate
0.3 M sodium formate
0.1 M sodium cacodylate pH 6.5
3% w/v PGA and 5% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.41 63.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.873 α = 90 b = 95.873 β = 90 c = 116.389 γ = 120
Symmetry Space Group P 32 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 PILATUS3 6M 2017-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 Diamond I04-1
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 2.61 83 100 0.127 0.134 0.043 0.998 9.4 9.6 19316 71.32
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 2.61 2.65 2.665 0.919 0.502 1
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 3TND 2.61 35.15 1.33 19115 931 99.07 0.2078 0.2064 0.2086 0.236 0.2417 80.58
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 12.3621 f_angle_d 0.4488 f_chiral_restr 0.0412 f_plane_restr 0.0032 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3164 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing