5FUX

catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FUVPDB ENTRY 5FUV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
170.1 M HEPES PH 7.0, 0.9 M SUCCINIC ACID, 1% (W/V) PEG 2K MME, 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
4.0470

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.76α = 90
b = 114.76β = 90
c = 104.45γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXELMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
12.243.921000.0718.912.3360452
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)
12.22.271001.222.311.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5FUV2.2114.7634261174999.970.188530.188090.1971RANDOM61.547
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]
-1.68-1.683.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.651
r_dihedral_angle_4_deg15.205
r_dihedral_angle_3_deg12.742
r_mcangle_it8.195
r_scbond_it8.152
r_dihedral_angle_1_deg6.726
r_mcbond_it6.277
r_mcbond_other6.256
r_angle_refined_deg2.076
r_angle_other_deg1.521
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.651
r_dihedral_angle_4_deg15.205
r_dihedral_angle_3_deg12.742
r_mcangle_it8.195
r_scbond_it8.152
r_dihedral_angle_1_deg6.726
r_mcbond_it6.277
r_mcbond_other6.256
r_angle_refined_deg2.076
r_angle_other_deg1.521
r_chiral_restr0.122
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.008
r_gen_planes_other0.008
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms2581
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing