6W3X | pdb_00006w3x

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

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	50.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.57	α = 90
b = 137.54	β = 94.49
c = 49.1	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		2016-10-07	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	1.4	28.18	94.3	0.047	11.4	3.2		103884

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	1.4	1.42			0.308	3.1

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	1.4	28.12	98569	5209	94.15	0.1147	0.1125	0.11	0.1543	0.16	RANDOM	16.811

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]
-0.16		0.21	-0.02		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.988
r_sphericity_free	34.778
r_dihedral_angle_4_deg	14.821
r_sphericity_bonded	14.532
r_dihedral_angle_3_deg	11.605
r_dihedral_angle_1_deg	6.475
r_rigid_bond_restr	5.352
r_angle_refined_deg	1.642
r_angle_other_deg	0.856
r_chiral_restr	0.117

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.988
r_sphericity_free	34.778
r_dihedral_angle_4_deg	14.821
r_sphericity_bonded	14.532
r_dihedral_angle_3_deg	11.605
r_dihedral_angle_1_deg	6.475
r_rigid_bond_restr	5.352
r_angle_refined_deg	1.642
r_angle_other_deg	0.856
r_chiral_restr	0.117
r_gen_planes_refined	0.015
r_bond_refined_d	0.012
r_gen_planes_other	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3968
Nucleic Acid Atoms
Solvent Atoms	902
Heterogen Atoms	38

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.