7SYB | pdb_00007syb

Crystal Structure of sulfurtransferase (DsrC family protein) from Acinetobacter baumannii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	290	AcbaC.18888.a.B1.PW38910 at 13 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 0.02M Calcium chloride dihydrate, 0.1M Sodium actetate pH 4.6, 30% v/v MPD (JCSG+ A4). Cryo: Direct. Puck: OKJ-1-3

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.5	α = 90
b = 46.84	β = 108.02
c = 39.48	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX-300	Beryllium Lenses	2021-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.45	29.29	99.6	0.047	0.054	0.999	16.25	4.074		20040			15.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.49	99.4		0.549	0.632	0.846	2.82	4.071

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.45	29.29	1.35	20034	1913	99.77	0.1416	0.1387	0.14	0.1684	0.17	20.984

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	826
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	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.