5DD7

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with AMPPNP and thiamine-monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5D9U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290Microlytic MGCS G4 optimization screen: 19% PEG 3350, 200mM KNa-tartrate, 100mM HEPES/NaOH pH 7.75; AcbaC.17905.a.B1.PW37686 at 30mg/ml with 5mM MgCl2/ANP, then over night soak with in reservoir solution with 5mM MgCl2/ANP/TMP; cryo: soak solution with 20% EG; tray 264486e7, puck RUX3-7
Crystal Properties
Matthews coefficientSolvent content
2.1743

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.96α = 90
b = 93.29β = 90
c = 73.48γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.75099.50.0530.05822.566.26641166088-318.91
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7499.20.5870.643.436.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5d9u1.739.411.3466070201599.50.15040.14950.1769Random selection26.7195
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.37
f_angle_d0.837
f_chiral_restr0.055
f_bond_d0.006
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4608
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms128

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction