3W3O | pdb_00003w3o

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-4-053

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3W2U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	298	0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.986	α = 90
b = 71.535	β = 90
c = 129.375	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	77	CCD	Bruker DIP-6040		2009-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	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	1.96	50	99.2	0.084	9.7	5.6	45625	45252		-3

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	1.97	2	99.4		0.398	5.04	5.6	2248

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	3W2U	1.96	27.53	45625	43256	2308	98.33	0.15138	0.15138	0.14916	0.16	0.19177	0.2	RANDOM	20.527

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	38.439
r_dihedral_angle_4_deg	18.842
r_dihedral_angle_3_deg	13.798
r_dihedral_angle_1_deg	6.659
r_angle_refined_deg	2.01
r_angle_other_deg	0.988
r_chiral_restr	0.115
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.439
r_dihedral_angle_4_deg	18.842
r_dihedral_angle_3_deg	13.798
r_dihedral_angle_1_deg	6.659
r_angle_refined_deg	2.01
r_angle_other_deg	0.988
r_chiral_restr	0.115
r_bond_refined_d	0.02
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4776
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	197

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.