4DLC

Crystal Structure of Trypanosoma brucei dUTPase with dUMP, MgF3- transition state analogue, and Mg2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DKBPDB ENTRY 4DKB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52900.2 M sodium/potassium tartrate, 0.1 M Bis-Tris propane, pH 8.5, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.2445.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.28α = 90
b = 68.28β = 90
c = 123.66γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

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
11.75948.28199.80.0730.0732212.729775297751124.1
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)
11.7591.899.80.7810.781112.22169

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 DIFFRACTIONREFINED 4DKBTHROUGHOUTPDB ENTRY 4DKB1.75948.282977529775149599.860.16680.16680.16540.194RANDOM26.3871
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]
0.610.61-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it36.964
r_scangle_it35.581
r_dihedral_angle_2_deg35.492
r_dihedral_angle_4_deg13.239
r_dihedral_angle_3_deg11.072
r_mcangle_it8.521
r_mcbond_it6.807
r_dihedral_angle_1_deg5.218
r_angle_refined_deg1.41
r_mcbond_other1.199
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it36.964
r_scangle_it35.581
r_dihedral_angle_2_deg35.492
r_dihedral_angle_4_deg13.239
r_dihedral_angle_3_deg11.072
r_mcangle_it8.521
r_mcbond_it6.807
r_dihedral_angle_1_deg5.218
r_angle_refined_deg1.41
r_mcbond_other1.199
r_angle_other_deg0.935
r_chiral_restr0.086
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 Atoms1750
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms27

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
REFMACphasing