☰ Navigation Tabs
Crystal structure of the GT domain of Clostridium difficile Toxin A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VKD PDB ENTRY 2VKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.2 M tripotassium citrate, 20% w/v PEG3350, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.08 α = 90 b = 153.03 β = 90 c = 66.26 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315r 2011-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93930 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.486 76.575 99.9 0.082 13.8 7 111159 111159 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.486 1.57 100 0.622 0.622 1.2 7
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2VKD 1.5 34.481 1.35 111083 108020 5388 99.83 0.191 0.1898 0.1861 0.2141 0.2106
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] -0.4773 -0.8385 1.3158
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.235 f_angle_d 1.001 f_chiral_restr 0.069 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4403 Nucleic Acid Atoms Solvent Atoms 686 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction MxCuBE data collection