2PRX | pdb_00002prx

Crystal structure of Thioesterase superfamily protein (ZP_00837258.1) from Shewanella loihica PV-4 at 1.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	277	NANODROP, 2.4M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP	8	277	NANODROP, 2.4M (NH4)2SO4, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.501	α = 90
b = 38.501	β = 90
c = 172.247	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2007-02-15	M	MAD
1	2		CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-02-23

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837	SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97927, 0.97941, 0.91162	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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
2	1.5	86.066	76.7	0.05	0.05	9.4	2.9		35176

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
2	1.5	1.54	61.3		0.183	0.183	4.1	2.7	2100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	FREE R	1.5	28.736	35176	35102	1811	72.7	0.203	0.199	0.199	0.19	0.277	0.26	RANDOM EXPANDED BY TWIN LAW	15.625

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]

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.065
s_similar_dist	0.064
s_zero_chiral_vol	0.041
s_non_zero_chiral_vol	0.041
s_from_restr_planes	0.027
s_angle_d	0.026
s_anti_bump_dis_restr	0.024
s_bond_d	0.008
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1705
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms

Software

Software
Software Name	Purpose
SHELX	refinement
MolProbity	model building
SOLVE	phasing
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXL-97	refinement

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.