4DK2 | pdb_00004dk2

Crystal Structure of Open Trypanosoma brucei dUTPase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OGLPDB ENTRY 1OGL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429025% PEG1500, 0.1 M MMT buffer, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1141.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.01α = 90
b = 47.02β = 89.38
c = 63.46γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.978DiamondI24

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
11.4742.0599.50.0720.0728.33.5472544725411
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)
11.471.5598.50.4930.4932.33.16789

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OGL1.4742.0514725444812236899.330.179330.177740.180.210680.21RANDOM20.009
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]
-0.69-0.261.05-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it65.748
r_mcbond_it61.494
r_mcangle_it48.884
r_scangle_it37.015
r_dihedral_angle_2_deg34.064
r_dihedral_angle_4_deg16.661
r_dihedral_angle_3_deg11.642
r_mcbond_other10.272
r_dihedral_angle_1_deg5.09
r_angle_refined_deg1.439
RMS Deviations
KeyRefinement Restraint Deviation
r_scbond_it65.748
r_mcbond_it61.494
r_mcangle_it48.884
r_scangle_it37.015
r_dihedral_angle_2_deg34.064
r_dihedral_angle_4_deg16.661
r_dihedral_angle_3_deg11.642
r_mcbond_other10.272
r_dihedral_angle_1_deg5.09
r_angle_refined_deg1.439
r_angle_other_deg0.951
r_chiral_restr0.093
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2008
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling