6H2F | pdb_00006h2f

Structure of the pre-pore AhlB of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		SeMet AhlB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	290	0.2 M ammonium phosphate 0.1 M Tris pH 8.5 50 % (v/v) MPD

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.661	α = 90
b = 178.184	β = 90
c = 485.581	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2014-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97949	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.55	39.55	100	0.188	0.122	6.6	6.4		165574

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.73	100		0.751	2.7	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	THROUGHOUT	SeMet AhlB	2.55	39.55	156934	8380	99.8	0.19497	0.19052	0.2	0.27844	0.28	RANDOM	39.264

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]
1.6			1.53		-3.13

RMS Deviations
Key	Refinement Restraint Deviation
r_mcbond_other	87.013
r_mcbond_it	87.01
r_long_range_B_refined	72.764
r_long_range_B_other	72.763
r_scbond_it	71.545
r_scbond_other	70.685
r_mcangle_it	69.2
r_mcangle_other	69.199
r_scangle_other	61.63
r_dihedral_angle_2_deg	40.419
r_dihedral_angle_4_deg	21.033
r_dihedral_angle_3_deg	18.195
r_dihedral_angle_1_deg	6.182
r_angle_refined_deg	1.568
r_angle_other_deg	0.983
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	24746
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing