2GVH

Crystal structure of Acyl-CoA hydrolase (15159470) from AGROBACTERIUM TUMEFACIENS at 2.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	8	277	10.0% iso-Propanol, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.133836	60.750973

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.209	α = 90
b = 121.209	β = 90
c = 81.844	γ = 90

Symmetry
Space Group	P 43

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 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2005-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97942	APS	23-ID-D

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	2.5	48.7	86.1	0.096	10.7	3.5		35343			59.625

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	2.5	2.59	55.1	55.1	0.508		2.5

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.5	48.71	35321	1773	86.07	0.227	0.22663	0.226	0.244	RANDOM	66.083

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]
-5.13			-5.13		10.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.575
r_dihedral_angle_4_deg	20.227
r_dihedral_angle_3_deg	16.311
r_scangle_it	6.949
r_dihedral_angle_1_deg	6.055
r_scbond_it	5.355
r_mcangle_it	2.779
r_mcbond_it	1.549
r_angle_refined_deg	1.41
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.575
r_dihedral_angle_4_deg	20.227
r_dihedral_angle_3_deg	16.311
r_scangle_it	6.949
r_dihedral_angle_1_deg	6.055
r_scbond_it	5.355
r_mcangle_it	2.779
r_mcbond_it	1.549
r_angle_refined_deg	1.41
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.258
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.196
r_metal_ion_refined	0.19
r_xyhbond_nbd_refined	0.093
r_chiral_restr	0.08
r_bond_refined_d	0.016
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5443
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
SHELXD	phasing
SHARP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.