2IBU | pdb_00002ibu

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

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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
2.39	48.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.249	α = 90
b = 106.569	β = 102.9
c = 101.497	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	2004-02-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8115	EMBL/DESY, HAMBURG	X11

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	1.9	19.46	99.9	0.068	0.068	16	4.3	122801	122616			25

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	1.9	2	100		0.347	0.347	4.3	4.2	17454

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1WL4	1.9	19.46	122615	116484	6131	100	0.16719	0.16559	0.1663	0.19772	0.1993	RANDOM	26.242

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]
-0.18		0.09	0.38		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.158
r_dihedral_angle_4_deg	14.565
r_dihedral_angle_3_deg	12.932
r_dihedral_angle_1_deg	8.071
r_scangle_it	2.197
r_mcangle_it	1.995
r_scbond_it	1.558
r_mcbond_it	1.428
r_angle_refined_deg	1.332
r_nbtor_refined	0.297
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.185
r_symmetry_hbond_refined	0.154
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11522
Nucleic Acid Atoms
Solvent Atoms	1171
Heterogen Atoms	202

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing