4E1T

X-ray crystal structure of the transmembrane beta-domain from invasin from Yersinia pseudotuberculosis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E1S	PDB ENTRY 4E1S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE MONOOLEIN	4	294	0.05 M sodium citrate, pH 3.8-4.4, 0.2 M lithium sulfate, 23-35% PEG400, LIPIDIC CUBIC PHASE MONOOLEIN, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.404	α = 90
b = 124.885	β = 90
c = 65.073	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	MARMOSAIC 300 mm CCD	K-B pair of biomorph mirrors	2011-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.034375	APS	23-ID-B

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	2.263	67.007	92.7	0.133	8.2	5.1	15222	14111	2.3	2.3

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	2.263	2.38	76.2		0.599		2.9	1133

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4E1S	2.263	29.787	15222	14016	709	90.55	0.1915	0.1915	0.188	0.2596	RANDOM	50.288

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]
1.46			1.15		-2.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.565
r_dihedral_angle_4_deg	21.553
r_dihedral_angle_3_deg	17.787
r_dihedral_angle_1_deg	6.926
r_scangle_it	3.913
r_scbond_it	2.566
r_angle_refined_deg	1.954
r_mcangle_it	1.444
r_mcbond_it	0.782
r_chiral_restr	0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.565
r_dihedral_angle_4_deg	21.553
r_dihedral_angle_3_deg	17.787
r_dihedral_angle_1_deg	6.926
r_scangle_it	3.913
r_scbond_it	2.566
r_angle_refined_deg	1.954
r_mcangle_it	1.444
r_mcbond_it	0.782
r_chiral_restr	0.13
r_bond_refined_d	0.017
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1960
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	283

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.