5H5K

ATP and CMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PBR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.52930.1M HEPES, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.4549.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.84α = 92
b = 51.863β = 92.3
c = 53.595γ = 112.22
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2012-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

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
12.33098.80.1426.833.91864139.5
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)
12.32.3498.20.5322.213.3

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 REPLACEMENTTHROUGHOUT2PBR2.3301758893997.930.197430.194490.25109RANDOM39.468
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]
-2.940.782.411.314.65-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.313
r_dihedral_angle_4_deg17.221
r_dihedral_angle_3_deg15.026
r_long_range_B_refined6.071
r_long_range_B_other6.071
r_dihedral_angle_1_deg6.07
r_scangle_other4.645
r_mcangle_it3.773
r_mcangle_other3.772
r_scbond_it3.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.313
r_dihedral_angle_4_deg17.221
r_dihedral_angle_3_deg15.026
r_long_range_B_refined6.071
r_long_range_B_other6.071
r_dihedral_angle_1_deg6.07
r_scangle_other4.645
r_mcangle_it3.773
r_mcangle_other3.772
r_scbond_it3.115
r_scbond_other3.108
r_mcbond_it2.508
r_mcbond_other2.508
r_angle_refined_deg1.669
r_angle_other_deg0.968
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2986
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing