2AHV

Crystal Structure of Acyl-CoA transferase from E. coli O157:H7 (YdiF)-thioester complex with CoA- 1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AHU	PDB Entry 2AHU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	293	16% (w/v) PEG 3350, 80 mM Na K tartarate, pH 7.5, Microbatch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.43	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.085	α = 90
b = 140.24	β = 108.22
c = 112.682	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	ADSC QUANTUM 315		2005-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.1	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	50	98.8	0.079	9	3.6	159093	159093			25.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	90.5		0.454	2	2.7	14536

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 2AHU	2	50	156370	142009	14361	97.24	0.207	0.1862	0.18232	0.22437	RANDOM	25.933

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]
1.17		0.93	-1.3		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.997
r_dihedral_angle_3_deg	13.114
r_dihedral_angle_4_deg	12.876
r_dihedral_angle_1_deg	5.752
r_scangle_it	2.372
r_scbond_it	1.476
r_angle_refined_deg	1.183
r_mcangle_it	0.957
r_mcbond_it	0.576
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.997
r_dihedral_angle_3_deg	13.114
r_dihedral_angle_4_deg	12.876
r_dihedral_angle_1_deg	5.752
r_scangle_it	2.372
r_scbond_it	1.476
r_angle_refined_deg	1.183
r_mcangle_it	0.957
r_mcbond_it	0.576
r_nbtor_refined	0.305
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.136
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15618
Nucleic Acid Atoms
Solvent Atoms	1474
Heterogen Atoms	192

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.