2E68

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2E6A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	18% PEG 3350, 1mM Oxonic acid potassium salt, 0.25M Hexammine cobalt trichloride, 0.1M cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.443	α = 90
b = 71.944	β = 90
c = 123.852	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 210		2005-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.38	50	97.5	0.084	10.5	4.6	126103	122937		1

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	1.38	1.43	98.9		0.396	4.26	4.6	12338

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2E6A	1.38	29.99	1	126157	116503	6159	97.23	0.16919	0.16846	0.18286	RANDOM	8.754

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.429
r_dihedral_angle_4_deg	17.26
r_dihedral_angle_3_deg	10.926
r_dihedral_angle_1_deg	5.513
r_scangle_it	2.356
r_scbond_it	1.482
r_angle_refined_deg	1.198
r_mcangle_it	0.873
r_mcbond_it	0.559
r_symmetry_hbond_refined	0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.429
r_dihedral_angle_4_deg	17.26
r_dihedral_angle_3_deg	10.926
r_dihedral_angle_1_deg	5.513
r_scangle_it	2.356
r_scbond_it	1.482
r_angle_refined_deg	1.198
r_mcangle_it	0.873
r_mcbond_it	0.559
r_symmetry_hbond_refined	0.33
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.262
r_nbd_refined	0.197
r_xyhbond_nbd_refined	0.116
r_chiral_restr	0.08
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4763
Nucleic Acid Atoms
Solvent Atoms	632
Heterogen Atoms	115

Software

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