5XAI

dTMP 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
2.4650.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.634α = 92.17
b = 52.118β = 92.1
c = 53.394γ = 111.14
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2012-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.0SPring-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
125092.70.04244.123.92655222.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0357.20.1270.9933.8

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 REPLACEMENTTHROUGHOUT2PBR25025215133592.380.188750.185870.24395RANDOM40.726
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]
-3.042.362.11.924.39-2.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.943
r_dihedral_angle_4_deg18.754
r_dihedral_angle_3_deg15.902
r_long_range_B_refined6.945
r_long_range_B_other6.944
r_scangle_other5.979
r_dihedral_angle_1_deg5.909
r_mcangle_it4.38
r_mcangle_other4.379
r_scbond_it4.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.943
r_dihedral_angle_4_deg18.754
r_dihedral_angle_3_deg15.902
r_long_range_B_refined6.945
r_long_range_B_other6.944
r_scangle_other5.979
r_dihedral_angle_1_deg5.909
r_mcangle_it4.38
r_mcangle_other4.379
r_scbond_it4.378
r_scbond_other4.33
r_mcbond_other3.39
r_mcbond_it3.389
r_angle_refined_deg1.854
r_angle_other_deg1.086
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.003
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 Atoms3010
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing