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Structure of P. vulgaris HigB toxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MCT PDB ENTRY 4MCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293.15 40% (w/v) polyethylene glycol monomethyl ether 2,000 and 0.15 M KBr, pH 7.5, VAPOR DIFFUSION, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 1.54 20.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.267 α = 90 b = 31.297 β = 112.18 c = 50.899 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 CCD MARMOSAIC 225 mm CCD 2012-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
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 1.25 15.71 99.7 0.05 19.3 7.2 23358 23296 -3 12.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.3 100 0.585 3.25 6.97 2593
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 (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 4MCT 1.25 15.71 2.02 23358 23290 2247 99.9 0.1579 0.155 0.1556 0.1893 0.1898 Random 17.75
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 12.895 f_angle_d 1.487 f_chiral_restr 0.069 f_bond_d 0.013 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 811 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 4
Software Software Software Name Purpose XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction SERGUI data collection XDS data reduction