5H56

ADP and dTDP 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
1VAPOR DIFFUSION, SITTING DROP6.52930.1M Bis-Tris pH 6.5, 45% MPD, 0.2M CaCl2, 10mM Mg, 10mM dTDP, 10mM ADP
Crystal Properties
Matthews coefficientSolvent content
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.482α = 90
b = 62.414β = 91.02
c = 76.144γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2007-09-24MSINGLE 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
11.75097.80.05445.674294022.6
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)
11.71.7682.30.1597.514.23578

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 REPLACEMENTTHROUGHOUT2PBR1.75040793212797.780.157360.155890.18525RANDOM14.244
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]
-0.08-0.351.02-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.205
r_dihedral_angle_4_deg17.36
r_dihedral_angle_3_deg11.813
r_dihedral_angle_1_deg5.161
r_long_range_B_refined3.862
r_long_range_B_other3.862
r_scangle_other2.25
r_angle_refined_deg1.569
r_mcangle_other1.429
r_mcangle_it1.428
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.205
r_dihedral_angle_4_deg17.36
r_dihedral_angle_3_deg11.813
r_dihedral_angle_1_deg5.161
r_long_range_B_refined3.862
r_long_range_B_other3.862
r_scangle_other2.25
r_angle_refined_deg1.569
r_mcangle_other1.429
r_mcangle_it1.428
r_scbond_it1.422
r_scbond_other1.422
r_angle_other_deg0.911
r_mcbond_it0.875
r_mcbond_other0.869
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms3073
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms128

Software

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