5XB3

ADP-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
1MICROBATCH72950.2M Ammonium citrate tribasic, 20% w/v Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.5551.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.54α = 90.97
b = 52.98β = 90.69
c = 53.78γ = 109.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9537ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.7753.76920.0730.99915.453957419.6
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)
11.771.8784.60.6040.8164.8

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 REPLACEMENTTHROUGHOUT2PBR1.7753.7637728184491.970.164850.162520.21263RANDOM20.547
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]
-0.79-0.251.130.411.590.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.841
r_dihedral_angle_4_deg17.935
r_dihedral_angle_3_deg14.319
r_dihedral_angle_1_deg5.991
r_long_range_B_refined5.092
r_long_range_B_other5.026
r_scangle_other4.242
r_scbond_it2.842
r_scbond_other2.826
r_mcangle_it2.423
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.841
r_dihedral_angle_4_deg17.935
r_dihedral_angle_3_deg14.319
r_dihedral_angle_1_deg5.991
r_long_range_B_refined5.092
r_long_range_B_other5.026
r_scangle_other4.242
r_scbond_it2.842
r_scbond_other2.826
r_mcangle_it2.423
r_mcangle_other2.423
r_angle_refined_deg2.082
r_mcbond_it1.749
r_mcbond_other1.74
r_angle_other_deg1.072
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms3080
Nucleic Acid Atoms
Solvent Atoms283
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing