5XBH

Crystal structure of R145E mutant 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
1MICROBATCH7.52950.2M Ammonium acetate, 0.1M HEPES, 25% w/v Polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.2144.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.82α = 97.01
b = 51.55β = 105.9
c = 51.76γ = 111.66
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2016-05-26MSINGLE 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)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
12.2148.291.20.0620.997153.91742827.8
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)
12.212.2964.90.2530.8964.93.6

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 REPLACEMENTTHROUGHOUT2PBR2.2348.21655483893.110.23120.228710.28113RANDOM28.873
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]
-1.1-0.110.39-0.340.680.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.713
r_dihedral_angle_4_deg20.784
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg5.818
r_long_range_B_refined3.002
r_long_range_B_other3.002
r_scangle_other1.782
r_mcangle_it1.595
r_mcangle_other1.595
r_angle_refined_deg1.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.713
r_dihedral_angle_4_deg20.784
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg5.818
r_long_range_B_refined3.002
r_long_range_B_other3.002
r_scangle_other1.782
r_mcangle_it1.595
r_mcangle_other1.595
r_angle_refined_deg1.206
r_scbond_it1.038
r_scbond_other1.037
r_mcbond_it0.94
r_mcbond_other0.937
r_angle_other_deg0.887
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
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 Atoms3138
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing