2IB9

Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase (T2): the importance of potassium and chloride for its structure and function

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WL4	PDB entry 1WL4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	18% PEG 5000 monomethylether, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.749	α = 90
b = 107.44	β = 103.06
c = 102.326	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	MAR CCD 165 mm	mirrors	2006-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.4022	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.05	73.72	99.9	0.073	0.073	16.3	4.1	100031	99949			27

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.15	99.9		0.357	0.357	3.9	4.1	13221

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1WL4	2.05	73.72	99951	94953	4998	100	0.15817	0.15601	0.1992	RANDOM	31.835

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]
-0.28		-0.34	0.34		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.621
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_4_deg	12.35
r_dihedral_angle_1_deg	5.604
r_scangle_it	2.142
r_mcangle_it	1.956
r_scbond_it	1.519
r_mcbond_it	1.302
r_angle_refined_deg	1.265
r_nbtor_refined	0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.621
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_4_deg	12.35
r_dihedral_angle_1_deg	5.604
r_scangle_it	2.142
r_mcangle_it	1.956
r_scbond_it	1.519
r_mcbond_it	1.302
r_angle_refined_deg	1.265
r_nbtor_refined	0.291
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.161
r_xyhbond_nbd_refined	0.124
r_symmetry_hbond_refined	0.11
r_chiral_restr	0.088
r_metal_ion_refined	0.053
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11512
Nucleic Acid Atoms
Solvent Atoms	938
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
XDS	data reduction
XDS	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.