2DJL | pdb_00002djl

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with succinate

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.154	α = 90
b = 71.766	β = 90
c = 123.4	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	Bruker DIP-6040		2005-06-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.90000	SPring-8	BL44XU

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	94.9	0.06	9	5.2	125392	118965		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	69.5		0.33	2.62	3.4	12383

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 (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 2E6A	1.38	50	1	125392	112910	5980	95.51	0.16612	0.16524	0.16	0.18277	0.18	RANDOM	12.021

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	37.232
r_dihedral_angle_4_deg	17.436
r_dihedral_angle_3_deg	10.446
r_dihedral_angle_1_deg	5.688
r_scangle_it	2.288
r_scbond_it	1.471
r_angle_refined_deg	1.192
r_mcangle_it	0.81
r_mcbond_it	0.507
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.232
r_dihedral_angle_4_deg	17.436
r_dihedral_angle_3_deg	10.446
r_dihedral_angle_1_deg	5.688
r_scangle_it	2.288
r_scbond_it	1.471
r_angle_refined_deg	1.192
r_mcangle_it	0.81
r_mcbond_it	0.507
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.309
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.099
r_chiral_restr	0.079
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4758
Nucleic Acid Atoms
Solvent Atoms	695
Heterogen Atoms	115

Software

Software
Software Name	Purpose
REFMAC	refinement
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.