3AAY

Crystal structure of probable thiosulfate sulfurtransferase CYSA3 (RV3117) from Mycobacterium tuberculosis: orthorhombic form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UAR	PDB ENTRY 1UAR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	Protein Concentration 8 mg/ml in Tris Buffer pH 7.5, Precipitant 0.1M Bis-Tris at pH 5.5, 3% MPD, 5mM sodium thiosulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.431	α = 90
b = 84.141	β = 90
c = 102.464	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	ADSC QUANTUM 315	Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)	2008-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.976067	SSRL	BL9-1

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	1.9	50	99.9	0.143	14	7.3	47968	47968

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	1.9	1.97	100		0.616	3.8	7.3	4717

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UAR	1.9	37	46409	46409	1486	99.83	0.19027	0.19027	0.18864	0.24187	RANDOM	25.376

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]
-0.51			-1.18		1.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.16
r_dihedral_angle_4_deg	18
r_dihedral_angle_3_deg	13.435
r_dihedral_angle_1_deg	5.97
r_scangle_it	3.322
r_scbond_it	2.024
r_angle_refined_deg	1.3
r_mcangle_it	1.3
r_mcbond_it	0.699
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.16
r_dihedral_angle_4_deg	18
r_dihedral_angle_3_deg	13.435
r_dihedral_angle_1_deg	5.97
r_scangle_it	3.322
r_scbond_it	2.024
r_angle_refined_deg	1.3
r_mcangle_it	1.3
r_mcbond_it	0.699
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4346
Nucleic Acid Atoms
Solvent Atoms	458
Heterogen Atoms	34

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.