2E68

Crystal structure of Trypanosoma cruzi dihydroorotate dehydrogenase in complex with dihydroorotate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E6A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP527718% 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 coefficientSolvent content
2.2344.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.443α = 90
b = 71.944β = 90
c = 123.852γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
11.385097.50.08410.54.61261031229371
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)
11.381.4398.90.3964.264.612338

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2E6A1.3829.991126157116503615997.230.169190.168460.18286RANDOM8.754
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.429
r_dihedral_angle_4_deg17.26
r_dihedral_angle_3_deg10.926
r_dihedral_angle_1_deg5.513
r_scangle_it2.356
r_scbond_it1.482
r_angle_refined_deg1.198
r_mcangle_it0.873
r_mcbond_it0.559
r_symmetry_hbond_refined0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.429
r_dihedral_angle_4_deg17.26
r_dihedral_angle_3_deg10.926
r_dihedral_angle_1_deg5.513
r_scangle_it2.356
r_scbond_it1.482
r_angle_refined_deg1.198
r_mcangle_it0.873
r_mcbond_it0.559
r_symmetry_hbond_refined0.33
r_nbtor_refined0.309
r_symmetry_vdw_refined0.262
r_nbd_refined0.197
r_xyhbond_nbd_refined0.116
r_chiral_restr0.08
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4763
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing