3PNX | pdb_00003pnx

Crystal structure of a putative sulfurtransferase dsrE (Swol_2425) from Syntrophomonas wolfei str. Goettingen at 1.92 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.67	277	0.80M sodium chloride, 24.00% polyethylene glycol 600, 10.00% Glycerol, 0.1M sodium cacodylate pH 6.67, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.416	α = 90
b = 76.504	β = 93.08
c = 127.652	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 325 mm CCD		2010-04-08	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97960,0.97925	SSRL	BL11-1

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	1.92	29.453	95.7	0.027	15.37			72995		-3	37.721

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	1.92	1.99	94.7		0.566	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	1.92	29.453	72993	3687	98.78	0.1909	0.1896	0.19	0.2152	0.22	RANDOM	51.769

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]
1.02		-1.01	-0.11		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.727
r_dihedral_angle_4_deg	22.188
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.323
r_scangle_it	3.273
r_scbond_it	1.938
r_mcangle_it	1.283
r_angle_refined_deg	1.218
r_angle_other_deg	0.837
r_mcbond_it	0.678

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.727
r_dihedral_angle_4_deg	22.188
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	5.323
r_scangle_it	3.273
r_scbond_it	1.938
r_mcangle_it	1.283
r_angle_refined_deg	1.218
r_angle_other_deg	0.837
r_mcbond_it	0.678
r_mcbond_other	0.138
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7354
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	36

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	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.