3W7D | pdb_00003w7d

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-5-170

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3W70	PDB ENTRY 3W70

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	277	0.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.994	α = 90
b = 71.567	β = 90
c = 129.346	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	ADSC QUANTUM 270		2009-11-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98	Photon Factory	BL-17A

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	1.52	50	99.2	0.065	10	5.5		96556		-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	1.52	1.55	100		0.433	3.18	5.4	4752

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 3W70	1.52	49.34	96480	4820	99.1	0.1464	0.145	0.17	0.1735	0.19	RANDOM	15.7625

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]
-0.1			-0.19		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.701
r_dihedral_angle_4_deg	19.455
r_dihedral_angle_3_deg	11.981
r_dihedral_angle_1_deg	6.925
r_angle_refined_deg	2.503
r_mcangle_it	2.294
r_mcbond_it	1.608
r_mcbond_other	1.607
r_angle_other_deg	1.265
r_chiral_restr	0.212

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.701
r_dihedral_angle_4_deg	19.455
r_dihedral_angle_3_deg	11.981
r_dihedral_angle_1_deg	6.925
r_angle_refined_deg	2.503
r_mcangle_it	2.294
r_mcbond_it	1.608
r_mcbond_other	1.607
r_angle_other_deg	1.265
r_chiral_restr	0.212
r_bond_refined_d	0.026
r_gen_planes_refined	0.016
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4776
Nucleic Acid Atoms
Solvent Atoms	674
Heterogen Atoms	215

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.