3QLB

Enantiopyochelin outer membrane TonB-dependent transporter from Pseudomonas fluorescens bound to the ferri-enantiopyochelin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BY3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	14% PEG1500, 0.1M lithium sulfate, 0.1M sodium citrate, 20% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.71	73.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.07	α = 90
b = 170.83	β = 90
c = 232.62	γ = 90

Symmetry
Space Group	C 2 2 21

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 315r	Mirrors	2010-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.95024	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.25	48.57	99.3	0.137	16.11	8.2	48366	48366		-3	78.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.26	3.34	96.4		0.659		8.1	3436

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1BY3	3.26	48.57	48332	45793	2426	99.03	0.21648	0.21648	0.21419	0.21	0.2588	0.26	RANDOM	70.493

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]
9.99			-1.69		-8.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.291
r_dihedral_angle_3_deg	21.368
r_dihedral_angle_4_deg	20.367
r_dihedral_angle_1_deg	7.688
r_scangle_it	2.741
r_angle_refined_deg	2.079
r_scbond_it	1.525
r_mcangle_it	1.228
r_mcbond_it	0.641
r_chiral_restr	0.118

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10449
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	80

Software

Software
Software Name	Purpose
X-NEMO	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

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.