5FUV

catalytic domain of Thymidine kinase from Trypanosoma brucei with dThd


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1W4RPDB ENTRY 1W4R

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 = 114.68α = 90
b = 114.68β = 90
c = 105.6γ = 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 I04DiamondI04

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
12.344.2599.90.081714.3318642
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)
12.32.3999.91.022.614.3

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 1W4R2.3114.6830146170899.810.180160.178690.20745RANDOM58.235
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]
-0.77-0.771.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.236
r_dihedral_angle_4_deg15.695
r_dihedral_angle_3_deg13.088
r_mcangle_it8.032
r_scbond_it7.735
r_dihedral_angle_1_deg6.603
r_mcbond_it5.985
r_mcbond_other5.979
r_angle_refined_deg2.217
r_angle_other_deg1.573
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.236
r_dihedral_angle_4_deg15.695
r_dihedral_angle_3_deg13.088
r_mcangle_it8.032
r_scbond_it7.735
r_dihedral_angle_1_deg6.603
r_mcbond_it5.985
r_mcbond_other5.979
r_angle_refined_deg2.217
r_angle_other_deg1.573
r_chiral_restr0.123
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d0.009
r_gen_planes_other0.007
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 Atoms2588
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing