2AHU | pdb_00002ahu

Crystal structure of Acyl-CoA transferase (YdiF) apoenzyme from Escherichia coli O157:H7.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	294	22.5 % (w/v) PEG 4000, 3% (v/v) isopropanol and 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.43	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.129	α = 90
b = 133.308	β = 100.57
c = 105.838	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 4	mirrors	2004-06-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 4	mirrors	2004-06-12	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.1	NSLS	X8C
2	SYNCHROTRON	NSLS BEAMLINE X8C	0.9799, 0.9795, 0.9646	NSLS	X8C

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	1.9	50	94.3	0.053	20.1	3	491266	163843

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	1.9	1.97	71.8		0.284	4.4	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.9	50	163804	148789	15015	94.34	0.19026	0.18714	0.1878	0.22044	0.2209	RANDOM	27.689

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]
0.78		0.27	-0.65		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.572
r_dihedral_angle_4_deg	15.175
r_dihedral_angle_3_deg	14.498
r_dihedral_angle_1_deg	5.321
r_scangle_it	2.759
r_scbond_it	1.808
r_angle_refined_deg	1.143
r_mcangle_it	1.048
r_mcbond_it	0.697
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.195
r_nbd_refined	0.184
r_symmetry_hbond_refined	0.136
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15696
Nucleic Acid Atoms
Solvent Atoms	1271
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing