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Crystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AHL PDB ENTRY 7AHL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289.15 12% PEG 4000, 100 mM Sodium cacodylate, 0.1 mM Polyethylene glycol dodecyl ether , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.15K
Crystal Properties Matthews coefficient Solvent content 4.24 71.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 313.23 α = 90 b = 168.04 β = 109.42 c = 160.46 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 RIGAKU SATURN 944 2012-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 3.9 27.7 97 0.344 3.7 3.7 71370 69515 40.9
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 3.9 4.11 97 0.685 2 3.7 10078
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 7AHL 3.9 27.7 1.42 67120 63875 3245 89.56 0.2851 0.2838 0.2844 0.3089 0.3085 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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.225 f_angle_d 0.832 f_chiral_restr 0.052 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27963 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing PHENIX refinement MOSFLM data reduction SCALA data scaling