4S2E

Phosphate ion bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.52930.1 M HEPES, 10% w/v Polyethylene glycol 8,000, 8% v/v Ethylene glycol , Microbatch Underoil, pH 7.5, EVAPORATION, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.4449.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.87α = 92.29
b = 51.78β = 92.83
c = 53.65γ = 112.76
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

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
12.354090.40.0518.54631361595433
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)
12.352.4892.30.1189.649345

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 REPLACEMENTTHROUGHOUT2PBR2.35401509482690.170.203770.200330.26664RANDOM32.711
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]
-2.690.572.070.274.440.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.12
r_dihedral_angle_4_deg21.785
r_dihedral_angle_3_deg14.686
r_dihedral_angle_1_deg6.044
r_long_range_B_refined5.434
r_long_range_B_other5.434
r_scangle_other3.977
r_mcangle_it3.461
r_mcangle_other3.461
r_scbond_it2.581
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.12
r_dihedral_angle_4_deg21.785
r_dihedral_angle_3_deg14.686
r_dihedral_angle_1_deg6.044
r_long_range_B_refined5.434
r_long_range_B_other5.434
r_scangle_other3.977
r_mcangle_it3.461
r_mcangle_other3.461
r_scbond_it2.581
r_scbond_other2.555
r_mcbond_other2.322
r_mcbond_it2.321
r_angle_refined_deg1.523
r_angle_other_deg0.847
r_chiral_restr0.076
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2987
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms10

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling