4DK4

Crystal Structure of Trypanosoma brucei dUTPase with dUpNp, Ca2+ and Na+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OGKPDB ENTRY 1OGK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729025% w/v PEG1500, 0.1 M PCB buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
1.7329

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.84α = 90
b = 83.19β = 90
c = 91.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42010-06-12SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.961.4551000.1070.10713.28.336008360081119.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.921000.5440.5441.47.35150

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OGK1.961.4553600835890179399.820.18010.18010.17740.2321RANDOM22.5685
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]
-0.650.66-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.597
r_scbond_it31.334
r_scangle_it17.995
r_mcangle_it15.028
r_dihedral_angle_4_deg13.052
r_mcbond_it12.662
r_dihedral_angle_3_deg11.806
r_dihedral_angle_1_deg5.28
r_angle_refined_deg1.434
r_angle_other_deg0.982
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.597
r_scbond_it31.334
r_scangle_it17.995
r_mcangle_it15.028
r_dihedral_angle_4_deg13.052
r_mcbond_it12.662
r_dihedral_angle_3_deg11.806
r_dihedral_angle_1_deg5.28
r_angle_refined_deg1.434
r_angle_other_deg0.982
r_mcbond_other0.413
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3364
Nucleic Acid Atoms
Solvent Atoms144
Heterogen Atoms54

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
APEXdata collection