6H2D

Structure of the soluble AhlC of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSeMet AhlC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82900.2 M Sodium chloride 0.1 M Tris pH 8 20 % (w/v) PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.2144.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.07α = 90
b = 61.66β = 92.01
c = 129.77γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97626DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.6246.7499.70.0740.058113.43115037.858
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.622.691000.710.5091.81.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSeMet AhlC2.6246.7429691144899.620.272180.269090.33432RANDOM55.841
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]
1.58-0.061.55-3.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.977
r_dihedral_angle_4_deg19.64
r_scbond_it19.578
r_scbond_other19.575
r_dihedral_angle_3_deg18.468
r_scangle_other16.218
r_long_range_B_refined13.776
r_long_range_B_other13.776
r_mcangle_it7.179
r_mcangle_other7.178
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.977
r_dihedral_angle_4_deg19.64
r_scbond_it19.578
r_scbond_other19.575
r_dihedral_angle_3_deg18.468
r_scangle_other16.218
r_long_range_B_refined13.776
r_long_range_B_other13.776
r_mcangle_it7.179
r_mcangle_other7.178
r_dihedral_angle_1_deg6.205
r_mcbond_it4.934
r_mcbond_other4.934
r_angle_refined_deg1.475
r_angle_other_deg0.955
r_chiral_restr0.068
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6152
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing