5FUW

catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP or dThd


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, 0.8 M SUCCINIC ACID 1 MM TMP, 1 MM APPNHP, 3 MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
3.7767

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.999α = 90
b = 114.999β = 90
c = 104.77γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE 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
12.264.241000.111.811.6362992
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)
12.22.271000.882.610.8

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 5FUV2.211534470175799.880.18610.185320.20126RANDOM55.707
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]
-1.23-1.232.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.005
r_dihedral_angle_3_deg12.572
r_long_range_B_refined12.472
r_long_range_B_other12.472
r_dihedral_angle_4_deg11.105
r_scangle_other10.463
r_mcangle_it7.817
r_mcangle_other7.815
r_scbond_it7.574
r_scbond_other7.409
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.005
r_dihedral_angle_3_deg12.572
r_long_range_B_refined12.472
r_long_range_B_other12.472
r_dihedral_angle_4_deg11.105
r_scangle_other10.463
r_mcangle_it7.817
r_mcangle_other7.815
r_scbond_it7.574
r_scbond_other7.409
r_dihedral_angle_1_deg6.675
r_mcbond_it5.71
r_mcbond_other5.706
r_angle_refined_deg2.16
r_angle_other_deg1.636
r_chiral_restr0.125
r_bond_refined_d0.022
r_gen_planes_refined0.013
r_bond_other_d0.009
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2577
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing