8ALO | pdb_00008alo

Heterodimer formation of sensory domains of Vibrio cholerae regulators ToxR and ToxS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		Alphafold Model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	30mg/ml of ToxRSp in Tris buffer (20mM Tris, 150mM NaCl, pH7), 0.5 microliters of protein was mixed with 0.5 microliters of crystal condition (0.2 M Magnesium chloride hexahydrate. 0.1 M BIS-Tris. 5.5. 25 % w/v PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.507	α = 90
b = 72.507	β = 90
c = 79.463	γ = 120

Symmetry
Space Group	P 65

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 EIGER X 4M		2016-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.967700	ESRF	BM30A

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	3	62.793	100	0.108	0.123	0.059	0.999	12.8	8.1		4790

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	3	3.18			0.842	0.966	0.466	0.688		7.8

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	Alphafold Model	3.002	62.793	4787	260	99.896	0.215	0.2129	0.21	0.2529	0.25	87.359

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]
-0.922	-0.461		-0.922		2.991

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.465
r_dihedral_angle_4_deg	22.217
r_dihedral_angle_3_deg	15.155
r_lrange_it	14.783
r_scangle_it	10.551
r_mcangle_it	8.9
r_dihedral_angle_1_deg	7.941
r_scbond_it	6.724
r_mcbond_it	5.626
r_angle_refined_deg	1.749
r_symmetry_xyhbond_nbd_refined	0.428
r_symmetry_nbd_refined	0.342
r_nbtor_refined	0.293
r_nbd_refined	0.213
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.071
r_bond_refined_d	0.013
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1854
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

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