6W3Y | pdb_00006w3y

Crystal structure of ligand-binding domain of Campylobacter jejuni chemoreceptor Tlp3 in complex with L-alanine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4XMR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	PEG 3350, sodium citrate and ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.565	α = 90
b = 137.618	β = 94.72
c = 49.118	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	CCD	ADSC QUANTUM 210r		2017-11-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9537	Australian Synchrotron	MX1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.32	46.12	97.5	0.026	15.9	3.5		128662

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.32	1.34			0.152	4.1

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	4xmr	1.32	46.12	122139	6471	97.41	0.1257	0.124	0.13	0.1562	0.16	RANDOM	20.369

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		-0.13	-0.48		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.533
r_dihedral_angle_2_deg	35.016
r_sphericity_bonded	14.438
r_dihedral_angle_4_deg	12.406
r_dihedral_angle_3_deg	11.862
r_dihedral_angle_1_deg	6.407
r_rigid_bond_restr	6.312
r_angle_refined_deg	1.485
r_angle_other_deg	1.073
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	35.533
r_dihedral_angle_2_deg	35.016
r_sphericity_bonded	14.438
r_dihedral_angle_4_deg	12.406
r_dihedral_angle_3_deg	11.862
r_dihedral_angle_1_deg	6.407
r_rigid_bond_restr	6.312
r_angle_refined_deg	1.485
r_angle_other_deg	1.073
r_chiral_restr	0.109
r_gen_planes_refined	0.015
r_bond_refined_d	0.012
r_gen_planes_other	0.007
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3966
Nucleic Acid Atoms
Solvent Atoms	799
Heterogen Atoms	36

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.