2IFC

The Structure of the Binary Complex of Oxalateacetate with Citrate Synthase from the Thermophilic Archaeon Thermolasma 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	8.5	280	17 % PEG 4000, 100mM Hepes 8.5, 200mM Sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.526	α = 90
b = 97.447	β = 93.1
c = 106.937	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	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	1.7	41.38	96.8	0.09	10	6.19	170739	170738

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	1.7	1.76	94.5		0.48	2.9	6.03	16592

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	1O7X_A	1.7	41.38	170707	170707	8560	96.77	0.183	0.181	0.234	RANDOM	26.348

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]
-0.17		-0.05	0.11		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.618
r_dihedral_angle_4_deg	15.864
r_dihedral_angle_3_deg	14.959
r_dihedral_angle_1_deg	5.562
r_scangle_it	3.921
r_scbond_it	2.619
r_angle_refined_deg	1.602
r_mcangle_it	1.563
r_mcbond_it	1.108
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.618
r_dihedral_angle_4_deg	15.864
r_dihedral_angle_3_deg	14.959
r_dihedral_angle_1_deg	5.562
r_scangle_it	3.921
r_scbond_it	2.619
r_angle_refined_deg	1.602
r_mcangle_it	1.563
r_mcbond_it	1.108
r_nbtor_refined	0.306
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.187
r_symmetry_vdw_refined	0.182
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.121
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11958
Nucleic Acid Atoms
Solvent Atoms	2228
Heterogen Atoms	36

Software

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