5AHS | pdb_00005ahs

3-Sulfinopropionyl-Coenzyme A (3SP-CoA) desulfinase from Advenella mimgardefordensis DPN7T: holo crystal structure with the substrate analog succinyl-CoA

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AF7	PDB ENTRY 5AF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4		CRYSTALS USED FOR X-RAY DIFFRACTION STUDIES WERE GROWN IN 24-WELL LINBRO PLATES (HAMPTON RESEARCH) BY VAPOUR DIFFUSION IN A HANGING DROP CONFIGURATION FROM 0.1 M BIS- TRIS PH 6.5 AND 5- 20 % PEG 3350 AT A PROTEIN CONCENTRATION OF 10 MG/ML, BY MIXING 2 UL OF THE PROTEIN SOLUTION WITH 2 UL MOTHER LIQUOR

Crystal Properties
Matthews coefficient	Solvent content
2.7	55.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.066	α = 90
b = 233.493	β = 90
c = 121.285	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M	KB MIRRORS	2013-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)		PETRA III, EMBL c/o DESY	P13 (MX1)

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	2.3	121.29	99.9	0.08	13.5	4.9		126487		2

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	2.3	2.34	99.9		0.95	2	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	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	MOLECULAR REPLACEMENT	PDB ENTRY 5AF7	2.3	116.746	1.91	126282	12133	98.97	0.2017	0.1995	0.2	0.2442	0.25

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.318
f_angle_d	0.617
f_chiral_restr	0.025
f_bond_d	0.002
f_plane_restr	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17832
Nucleic Acid Atoms
Solvent Atoms	1462
Heterogen Atoms	571

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	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.