X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherT. acidophilum isopentenyl phosphate kinase solved by single wavelength anomalous diffraction

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62740.1 M PCB buffer (2:1:2 molar ratio of sodium propionate, sodium cacodylate, Bis-Tris propane, pH 6.0 containing 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 274K
Crystal Properties
Matthews coefficientSolvent content
2.2144.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 187.104α = 90
b = 42.787β = 113.19
c = 134.895γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)2009-02-27MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97887SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.99500.0629.481.865826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.992.060.0623.31.7

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTT. acidophilum isopentenyl phosphate kinase solved by single wavelength anomalous diffraction1.98738.2921.346916965826334295.960.19540.1930.2384
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]
0.5158-3.4756-1.33650.8207
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.754
f_angle_d1.975
f_chiral_restr0.115
f_bond_d0.021
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7261
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms164

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling