2R26 | pdb_00002r26

The Structure of the Ternary Complex of Carboxymethyl Coenzyme A and Oxalateacetate with Citrate Synthase from the Thermophilic Archaeonthermoplasma Acidophilum

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O7X	1O7X_A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	280	15-18% Peg 400, 100mM Hepes 7-8.5, 200 mM Sodium Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.705	α = 99.34
b = 74.221	β = 98.34
c = 89.874	γ = 114.38

Symmetry
Space Group	P 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	NOIR-1	DOUBLE CRYSTAL	2006-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.0000	ALS	4.2.2

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	2.4	43.09	97.5	0.101	6.1	3.17	59729	58219

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1O7X_A	2.5	43.09	51542	2604	97.52	0.203	0.203	0.2	0.2	0.261	RANDOM	37.683

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]
-1.23	-3.99	-1.25	-1.48	1.25	-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.822
r_dihedral_angle_3_deg	15.404
r_dihedral_angle_4_deg	12.564
r_dihedral_angle_1_deg	4.626
r_angle_refined_deg	0.981
r_scangle_it	0.83
r_mcangle_it	0.484
r_scbond_it	0.479
r_nbtor_refined	0.295
r_mcbond_it	0.268

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.822
r_dihedral_angle_3_deg	15.404
r_dihedral_angle_4_deg	12.564
r_dihedral_angle_1_deg	4.626
r_angle_refined_deg	0.981
r_scangle_it	0.83
r_mcangle_it	0.484
r_scbond_it	0.479
r_nbtor_refined	0.295
r_mcbond_it	0.268
r_nbd_refined	0.175
r_symmetry_vdw_refined	0.142
r_symmetry_hbond_refined	0.111
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11965
Nucleic Acid Atoms
Solvent Atoms	959
Heterogen Atoms	244

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
CNS	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.