3EH7

The structure of a putative 4-hydroxybutyrate CoA-transferase from Porphyromonas gingivalis W83

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	0.2M MgCl2, 0.1M Tris pH8.5, 16% PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.704	α = 90
b = 72.704	β = 90
c = 133.694	γ = 120

Symmetry
Space Group	P 32 1 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	CCD	ADSC QUANTUM 315		2006-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97922	APS	19-ID

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	2.05	44.56	99.6	0.12	6.3	11		25521		-3	30.5

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	2.052	2.105	96.83		0.623	2.7	7

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.05	44.56	25521	25521	1299	99.6	0.173	0.173	0.171	0.208	RANDOM	26.712

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]
-1.85	-0.92		-1.85		2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.862
r_dihedral_angle_4_deg	21.112
r_dihedral_angle_3_deg	15.067
r_dihedral_angle_1_deg	5.87
r_scangle_it	3.533
r_scbond_it	2.187
r_angle_refined_deg	1.413
r_mcangle_it	1.287
r_angle_other_deg	0.908
r_mcbond_it	0.702

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.862
r_dihedral_angle_4_deg	21.112
r_dihedral_angle_3_deg	15.067
r_dihedral_angle_1_deg	5.87
r_scangle_it	3.533
r_scbond_it	2.187
r_angle_refined_deg	1.413
r_mcangle_it	1.287
r_angle_other_deg	0.908
r_mcbond_it	0.702
r_mcbond_other	0.172
r_chiral_restr	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3060
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

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 R01GM133198.