6Z5H | pdb_00006z5h

Crystal structure of Aeromonas exotoxin A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IKQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	289	12 % v/v polyethylene glycol 6000, 0.1 M MES pH 5.5, 0.1 M ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.371	α = 90
b = 140.215	β = 101.793
c = 96.821	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS EIGER2 XE 16M		2019-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.3	56.36	99	0.128	0.14	0.055	0.998	12.5	12.6		60033			32.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	87.2		0.845	0.946	0.414	0.895	2.8	9.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1IKQ	2.3	49.575	59929	2999	98.86	0.206	0.2042	0.21	0.2471	0.25	37.252

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]
1.517		-2.045	-2.02		1.249

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.477
r_dihedral_angle_4_deg	16.035
r_dihedral_angle_3_deg	12.699
r_lrange_it	6.618
r_lrange_other	6.616
r_dihedral_angle_1_deg	6.467
r_scangle_it	4.32
r_scangle_other	4.32
r_mcangle_it	3.882
r_mcangle_other	3.882
r_scbond_it	2.608
r_scbond_other	2.607
r_mcbond_it	2.329
r_mcbond_other	2.329
r_angle_refined_deg	1.331
r_angle_other_deg	1.18
r_metal_ion_refined	0.376
r_nbd_refined	0.197
r_symmetry_nbd_other	0.178
r_nbd_other	0.172
r_xyhbond_nbd_refined	0.15
r_nbtor_refined	0.149
r_symmetry_xyhbond_nbd_refined	0.144
r_symmetry_nbd_refined	0.142
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.053
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9193
Nucleic Acid Atoms
Solvent Atoms	323
Heterogen Atoms	20

Software

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