1OGK

The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.625% PEG 2000 MME, 0.3M SODIUM FORMATE, 50 MM SODIUM HEPES PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.345.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.386α = 90
b = 50.307β = 101.35
c = 111.387γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2001-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.852099.70.0859.463.527211
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)
12.852.997.30.4421.13

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 REPLACEMENTTHROUGHOUTNATIVE STRUCTURE2.85111.825841136299.10.2090.2050.273RANDOM34.97
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]
-4.71.184.151.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.222
r_scangle_it2.78
r_angle_refined_deg1.931
r_scbond_it1.618
r_mcangle_it1.247
r_angle_other_deg1.019
r_mcbond_it0.65
r_symmetry_vdw_other0.257
r_nbd_other0.25
r_nbd_refined0.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.222
r_scangle_it2.78
r_angle_refined_deg1.931
r_scbond_it1.618
r_mcangle_it1.247
r_angle_other_deg1.019
r_mcbond_it0.65
r_symmetry_vdw_other0.257
r_nbd_other0.25
r_nbd_refined0.245
r_xyhbond_nbd_refined0.189
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.151
r_nbtor_other0.101
r_chiral_restr0.094
r_bond_refined_d0.02
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7712
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing