3LN6 | pdb_00003ln6

Crystal structure of a bifunctional glutathione synthetase from Streptococcus agalactiae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V4G	1V4G, 1UC8
experimental model	PDB	1UC8	1V4G, 1UC8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	1.6M (NH4)2SO4, 100mM Tris-HCl pH 8.5, 12% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.15	60.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.02	α = 90
b = 143.02	β = 90
c = 211.23	γ = 90

Symmetry
Space Group	I 41 2 2

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	MAR CCD 165 mm		2007-02-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210r		2008-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.0720	EMBL/DESY, HAMBURG	BW7A
2	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9330	ESRF	ID14-2

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	2.9	20	99.6	0.077	23.9	8.4		24531		-3	76.731

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)
	2.9	2.98	98.1		0.132	1.8	8.1	1765

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS, MR	THROUGHOUT	1V4G, 1UC8	2.95	20	23309	1178	99.9	0.253	0.25	0.286	0.28	RANDOM	95.45

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]
-1.03			-1.03		2.07

RMS Deviations
Key	Refinement Restraint Deviation
f_angle_d	1.512
f_bond_d	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5467
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	5

Software

Software
Software Name	Purpose
XSCALE	data processing
SOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
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 R01GM157729.