6H2F

Structure of the pre-pore AhlB 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 AhlB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52900.2 M ammonium phosphate 0.1 M Tris pH 8.5 50 % (v/v) MPD
Crystal Properties
Matthews coefficientSolvent content
3.2962.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.661α = 90
b = 178.184β = 90
c = 485.581γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

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
12.5539.551000.1880.1226.66.4165574
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.731000.7512.76.6

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 AhlB2.5539.55156934838099.80.194970.190520.27844RANDOM39.264
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]
1.61.53-3.13
RMS Deviations
KeyRefinement Restraint Deviation
r_mcbond_other87.013
r_mcbond_it87.01
r_long_range_B_refined72.764
r_long_range_B_other72.763
r_scbond_it71.545
r_scbond_other70.685
r_mcangle_it69.2
r_mcangle_other69.199
r_scangle_other61.63
r_dihedral_angle_2_deg40.419
RMS Deviations
KeyRefinement Restraint Deviation
r_mcbond_other87.013
r_mcbond_it87.01
r_long_range_B_refined72.764
r_long_range_B_other72.763
r_scbond_it71.545
r_scbond_other70.685
r_mcangle_it69.2
r_mcangle_other69.199
r_scangle_other61.63
r_dihedral_angle_2_deg40.419
r_dihedral_angle_4_deg21.033
r_dihedral_angle_3_deg18.195
r_dihedral_angle_1_deg6.182
r_angle_refined_deg1.568
r_angle_other_deg0.983
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms24746
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing