6R1J

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6H2E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8289.150.1M imidazole pH 8.0, 10% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.9458.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.538α = 90
b = 88.538β = 90
c = 290.975γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103PIXELDECTRIS PILATUS3 6M2018-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.976.861000.99716.118.752765
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9

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 REPLACEMENTTHROUGHOUT6H2E1.9276.685008925501000.236580.234490.27796RANDOM46.904
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]
0.750.370.75-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.544
r_dihedral_angle_4_deg15.059
r_dihedral_angle_3_deg12.005
r_long_range_B_other8.423
r_long_range_B_refined8.409
r_scangle_other6.776
r_mcangle_it5.819
r_mcangle_other5.818
r_scbond_it4.784
r_scbond_other4.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.544
r_dihedral_angle_4_deg15.059
r_dihedral_angle_3_deg12.005
r_long_range_B_other8.423
r_long_range_B_refined8.409
r_scangle_other6.776
r_mcangle_it5.819
r_mcangle_other5.818
r_scbond_it4.784
r_scbond_other4.783
r_mcbond_it4.311
r_mcbond_other4.31
r_dihedral_angle_1_deg3.283
r_angle_refined_deg1.613
r_angle_other_deg1.427
r_chiral_restr0.084
r_bond_refined_d0.009
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 Atoms3881
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing