4GXZ | pdb_00004gxz

Crystal structure of a periplasmic thioredoxin-like protein from Salmonella enterica serovar Typhimurium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GYK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.2	298	18-27% (w/v) PEG 4000, 0.1M Tris buffer pH 8.2 , VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.107	α = 90
b = 90.998	β = 102.23
c = 83.309	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		IMAGE PLATE	RIGAKU RAXIS IV++		2011-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.541

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	1.98	48.69	99.97	0.065	13	7.45	106172	106150	3	3	35.41

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	1.98	2.05	100		0.479	2.4	7.29	10617

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	3GYK	2.04	48.689	49333	49220	2506	99.77	0.2018	0.2018	0.1992	0.19	0.2526	0.24	RANDOM	44.5163

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]
-9.5202		-1.0006	-2.7511		12.2714

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.653
f_angle_d	1.003
f_chiral_restr	0.07
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5462
Nucleic Acid Atoms
Solvent Atoms	411
Heterogen Atoms

Software

Software
Software Name	Purpose
CrystalClear	data collection
BALBES	phasing
PHENIX	refinement
CrystalClear	data reduction
CrystalClear	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.