6PNV

1.42 Angstrom Resolution Crystal Structure of Translocation Protein TolB from Salmonella enterica

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein: 5.2 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (G4), 0.2 M Potassium thiocyanate, 0.1 M Bis Tris propane pH 7.5, 20% (w/v) PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.894	α = 90
b = 40.57	β = 111.61
c = 77.994	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	MARMOSAIC 300 mm CCD	C(111)	2019-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.42	30	96.2	0.054	0.054	0.062	0.029	22.8	4.2		67628		-3	13.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44	100		0.622	0.622	0.726	0.368	0.709	2.1	3.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2w8b	1.42	29.7	64124	3474	95.83	0.1635	0.1618	0.1944	RANDOM	16.254

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]
1.22		-0.7	-0.29		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.75
r_dihedral_angle_4_deg	10.771
r_dihedral_angle_3_deg	9.774
r_dihedral_angle_1_deg	4.512
r_angle_refined_deg	1.423
r_rigid_bond_restr	0.983
r_angle_other_deg	0.409
r_chiral_restr	0.065
r_gen_planes_refined	0.053
r_gen_planes_other	0.049

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.75
r_dihedral_angle_4_deg	10.771
r_dihedral_angle_3_deg	9.774
r_dihedral_angle_1_deg	4.512
r_angle_refined_deg	1.423
r_rigid_bond_restr	0.983
r_angle_other_deg	0.409
r_chiral_restr	0.065
r_gen_planes_refined	0.053
r_gen_planes_other	0.049
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3101
Nucleic Acid Atoms
Solvent Atoms	477
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
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 R01GM133198.