2J87

Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52-7% POLYETHYLENE GLYCOL 3350, 5MM MGSO4 AND 50MM MES PH6.5, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.2946.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.331α = 90
b = 63.331β = 90
c = 166.412γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATE2005-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
13.13094.80.158.53.8136362.3
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)
13.13.2187.90.492.32.8

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 1W4R3.1301214463794.30.2580.2570.289RANDOM42.97
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]
3.691.843.69-5.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.436
r_dihedral_angle_3_deg17.464
r_dihedral_angle_4_deg15.437
r_dihedral_angle_1_deg6.01
r_angle_refined_deg1.426
r_scangle_it0.827
r_scbond_it0.485
r_symmetry_vdw_refined0.483
r_mcangle_it0.327
r_nbtor_refined0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.436
r_dihedral_angle_3_deg17.464
r_dihedral_angle_4_deg15.437
r_dihedral_angle_1_deg6.01
r_angle_refined_deg1.426
r_scangle_it0.827
r_scbond_it0.485
r_symmetry_vdw_refined0.483
r_mcangle_it0.327
r_nbtor_refined0.32
r_nbd_refined0.27
r_mcbond_it0.19
r_xyhbond_nbd_refined0.178
r_symmetry_hbond_refined0.149
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms5206
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing