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Full-length structure of the Vibrio cholerae virulence activator, AphB, a member of the LTTR protein family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SEMET DERIVATIVE SOLVED BY SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 4 M sodium formate, 0.01 M betaine monohydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.34 63.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.209 α = 90 b = 106.1 β = 90 c = 167.846 γ = 90
Symmetry Space Group I 2 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 CCD MARMOSAIC 300 mm CCD 2006-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 48.9 99.8 13.12 4.9 45623 45546 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 99.4 4.1 4.9 7282
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 SEMET DERIVATIVE SOLVED BY SAD 2.202 48.85 2.01 45623 45542 2277 99.84 0.2093 0.208 0.2121 0.2345 0.2368 RANDOM
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] -3.1645 -3.4311 6.5956
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.424 f_angle_d 1.112 f_chiral_restr 0.073 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4629 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms
Software Software Software Name Purpose JBluIce-EPICS data collection PHENIX model building PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing