4DKB

Crystal Structure of Trypanosoma brucei dUTPase with dUpNp and Ca2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DK4PDB ENTRY 4DK4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729020% w/v PEG3350, 0.2 M ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.2545.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.47α = 90
b = 68.47β = 90
c = 123.87γ = 90
Symmetry
Space GroupP 43 21 2

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
11.83148.4161000.110.1118.513.726775267751120.1
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)
11.8311.931000.5840.5841.313.13824

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 4DK41.83148.4162667526675133199.860.17020.17020.16880.1978RANDOM21.4041
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]
0.050.05-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.899
r_scbond_it28.336
r_scangle_it24.393
r_dihedral_angle_3_deg13.111
r_mcangle_it12.524
r_mcbond_it11.51
r_dihedral_angle_4_deg10.979
r_dihedral_angle_1_deg4.918
r_angle_refined_deg1.44
r_angle_other_deg0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.899
r_scbond_it28.336
r_scangle_it24.393
r_dihedral_angle_3_deg13.111
r_mcangle_it12.524
r_mcbond_it11.51
r_dihedral_angle_4_deg10.979
r_dihedral_angle_1_deg4.918
r_angle_refined_deg1.44
r_angle_other_deg0.95
r_mcbond_other0.575
r_chiral_restr0.093
r_bond_refined_d0.017
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 Atoms1761
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms26

Software

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