3CE7 | pdb_00003ce7

Crystal structure of toxoplasma specific mitochondrial acyl carrier protein, 59.m03510

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L0I	PDB entry 1L0I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	1.5 M NH4SO4, 0.2 M K,Na Tartrate, 0.1 M Na Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.89	35.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.696	α = 90
b = 64.696	β = 90
c = 38.139	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2008-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	1.64	50	99.3	0.052	0.056	21.5	9.7	11276	11276			23.5

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)
	1.64	1.7	93.2		0.198	0.183	6.18	4.1	1054

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 (All)	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 1L0I	1.64	32.34	11265	11265	539	99.07	0.187	0.187	0.185	0.19	0.227	0.22	RANDOM	23.535

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]
-0.81	-0.41		-0.81		1.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.587
r_dihedral_angle_4_deg	13.733
r_dihedral_angle_3_deg	12.161
r_dihedral_angle_1_deg	4.387
r_scangle_it	3.06
r_scbond_it	1.92
r_mcangle_it	1.195
r_angle_refined_deg	1.072
r_mcbond_it	0.671
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.587
r_dihedral_angle_4_deg	13.733
r_dihedral_angle_3_deg	12.161
r_dihedral_angle_1_deg	4.387
r_scangle_it	3.06
r_scbond_it	1.92
r_mcangle_it	1.195
r_angle_refined_deg	1.072
r_mcbond_it	0.671
r_nbtor_refined	0.308
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.186
r_symmetry_hbond_refined	0.131
r_xyhbond_nbd_refined	0.099
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	741
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.