4MDC | pdb_00004mdc

Crystal structure of glutathione S-transferase from Sinorhizobium meliloti 1021, NYSGRC target 021389

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 ul of 12.6 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 0.2 ul of The Cryos Suite condition #80 (8.5% PEG 1000; 8.5% PEG 8000; 15% glycerol) and equilibrated against 1.9 M NaCl in QIAGEN EasyXtal 15-Well Tool plate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.181	α = 90
b = 53.508	β = 115.88
c = 111.123	γ = 90

Symmetry
Space Group	C 1 2 1

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	BE-LENSES	2013-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.78	50	99.9	0.075	10.5	5.2	93260	93167		-3	24

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)
1	1.78	1.81	100		0.721	0.721	2.1	5.2	4595

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.78	29.8	92782	92699	4636	99.91	0.1629	0.1614	0.16	0.1904	0.19	RANDOM	30.2278

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]
-2.02		-2.07	-0.44		2.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.598
r_dihedral_angle_4_deg	18.221
r_dihedral_angle_3_deg	14.189
r_dihedral_angle_1_deg	5.643
r_angle_refined_deg	1.68
r_angle_other_deg	1.536
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.598
r_dihedral_angle_4_deg	18.221
r_dihedral_angle_3_deg	14.189
r_dihedral_angle_1_deg	5.643
r_angle_refined_deg	1.68
r_angle_other_deg	1.536
r_chiral_restr	0.102
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.01
r_gen_planes_other	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7512
Nucleic Acid Atoms
Solvent Atoms	904
Heterogen Atoms	18

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
SOLVE	phasing
RESOLVE	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.