3W84

Structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with MII-6-101


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3W7MPDB ENTRY 3W7M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.22770.1M Cacodylate, 13% PEG3350, 0.05M Hexaamminecobalt (III) Chloride, 1mM Oxonate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3347.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.276α = 90
b = 71.676β = 90
c = 129.906γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARMOSAIC 225 mm CCD2010-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.933099.50.1387.86.948677-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9321000.4037.697.14814

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3W7M1.9329.3448326244198.620.2020.19920.2543RANDOM17.7418
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]
-0.2-0.550.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.88
r_dihedral_angle_4_deg20.787
r_dihedral_angle_3_deg13.352
r_dihedral_angle_1_deg6.645
r_mcangle_it1.97
r_angle_refined_deg1.88
r_mcbond_it1.291
r_mcbond_other1.272
r_angle_other_deg0.994
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.88
r_dihedral_angle_4_deg20.787
r_dihedral_angle_3_deg13.352
r_dihedral_angle_1_deg6.645
r_mcangle_it1.97
r_angle_refined_deg1.88
r_mcbond_it1.291
r_mcbond_other1.272
r_angle_other_deg0.994
r_chiral_restr0.107
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4776
Nucleic Acid Atoms
Solvent Atoms481
Heterogen Atoms189

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection