8OXS | pdb_00008oxs

Cholera holotoxin variant (chimera with E. coli heat-labile enterotoxin, 4 C-terminal substitutions)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1S5E	stripped of solvent and ligand molecules, used one copy of the holotoxin (1 A subunit, 5 B subunits) as the search model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293.15	Crystallization mix: 20% w/v PEG 6K 0.1 M HEPES pH 7.0 0.2 M NH4Cl Protein storage buffer: 0.05 M Tris/HCl pH 7.5 0.2 M NaCl 0.05 M D-(+)-galactose

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.295	α = 90
b = 89.61	β = 98.186
c = 141.094	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 PILATUS 2M-F		2022-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87313	ESRF	ID23-2

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	1.6	48.9	99.9	0.18	0.196	0.076	0.995	6.6	6.7		195625			21.6

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	1.6	1.63	99.7		1	1	1	0.997	0.6	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.6	48.9	195625	2055	99.781	0.194	0.1932	0.2	0.2239	0.23	23.729

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]
-0.714		0.019	2.141		-1.376

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.6
r_dihedral_angle_3_deg	14.264
r_dihedral_angle_2_deg	8.16
r_dihedral_angle_1_deg	7.1
r_lrange_it	4.914
r_lrange_other	4.914
r_scangle_it	3.35
r_scangle_other	3.35
r_mcangle_it	2.424
r_mcangle_other	2.424
r_scbond_it	2.094
r_scbond_other	2.094
r_mcbond_it	1.555
r_mcbond_other	1.555
r_angle_refined_deg	1.445
r_angle_other_deg	0.489
r_nbd_refined	0.211
r_symmetry_nbd_other	0.186
r_nbd_other	0.183
r_nbtor_refined	0.173
r_symmetry_nbd_refined	0.163
r_symmetry_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_refined	0.151
r_metal_ion_refined	0.121
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.029
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11848
Nucleic Acid Atoms
Solvent Atoms	764
Heterogen Atoms	266

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building
MxCuBE	data collection