5XB5

Crystal structure of R90A 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
1MICROBATCH7.52930.1M HEPES, 10% w/v Polyethylene glycol 8000, 8% v/v Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.4650.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.01α = 92.17
b = 51.84β = 92.67
c = 53.64γ = 112.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2012-04-10MSINGLE 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
12.2153.48930.10.99611.84.31975128.3
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)
12.212.2968.60.5540.8512.33.9

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 REPLACEMENTTHROUGHOUT2PBR2.2353.481875399195.010.242660.240350.28591RANDOM55.258
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]
-6.62.88-0.24.732.66-2.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.171
r_dihedral_angle_4_deg20.844
r_dihedral_angle_3_deg17.441
r_dihedral_angle_1_deg7.354
r_long_range_B_refined4.902
r_long_range_B_other4.902
r_angle_refined_deg1.855
r_angle_other_deg1.136
r_mcangle_it1.024
r_mcangle_other1.024
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.171
r_dihedral_angle_4_deg20.844
r_dihedral_angle_3_deg17.441
r_dihedral_angle_1_deg7.354
r_long_range_B_refined4.902
r_long_range_B_other4.902
r_angle_refined_deg1.855
r_angle_other_deg1.136
r_mcangle_it1.024
r_mcangle_other1.024
r_scangle_other0.89
r_mcbond_it0.558
r_mcbond_other0.556
r_scbond_it0.546
r_scbond_other0.545
r_chiral_restr0.106
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms2974
Nucleic Acid Atoms
Solvent Atoms38
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing