3IR4 | pdb_00003ir4

1.2 Angstrom Crystal Structure of the Glutaredoxin 2 (grxB) from Salmonella typhimurium in complex with Glutathione

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	295	Protein solution: 0.3M Sodium chloride, 10mM HEPES (pH 7.5); Screen solution: 0.1M Sodium citrate (pH 5.6), 2M Ammonium sulphate, 0.2M Sodium-Potassium tartrate, 5mM Glutathione, 4% (w/v) Sucrose; Cryo solution: paratone, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.24	α = 90
b = 58.76	β = 90
c = 87.93	γ = 90

Symmetry
Space Group	P 21 21 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	Mirrors	2009-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07810	APS	21-ID-D

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	1.2	30	98.7	0.079	14.93	5.73	66655	66655		-3	6.7

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	1.2	1.22	96.7		0.496	4.04	5.46	3133

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	SAD	THROUGHOUT	1.2	27.87	63340	63340	3315	98.65	0.11808	0.11808	0.11671	0.1162	0.14426	0.1436	RANDOM	6.29

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]
-0.28			0.15		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.367
r_dihedral_angle_4_deg	13.454
r_dihedral_angle_3_deg	10.531
r_dihedral_angle_1_deg	4.801
r_scangle_it	4.689
r_scbond_it	3.281
r_mcangle_it	2.032
r_rigid_bond_restr	1.62
r_angle_refined_deg	1.502
r_mcbond_it	1.449

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.367
r_dihedral_angle_4_deg	13.454
r_dihedral_angle_3_deg	10.531
r_dihedral_angle_1_deg	4.801
r_scangle_it	4.689
r_scbond_it	3.281
r_mcangle_it	2.032
r_rigid_bond_restr	1.62
r_angle_refined_deg	1.502
r_mcbond_it	1.449
r_mcbond_other	1.396
r_angle_other_deg	0.958
r_chiral_restr	0.1
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1740
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	36

Software

Software
Software Name	Purpose
Blu-Ice	data collection
CRANK	phasing
REFMAC	refinement
XDS	data reduction
XDS	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.