3SK3

Crystal structure of Salmonella typhimurium acetate kinase (AckA) with citrate bound at the dimeric interface


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IIRPDB ENTRY 2IIR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1UNDER-OIL MICROBATCH7.52980.1M HEPES, 1.4M Sodium citrate, pH 7.5, UNDER-OIL MICROBATCH, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8757.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.012α = 90
b = 78.5β = 116.37
c = 97.48γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDBent collimating mirror and toroid2009-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.95ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.95098.60.06215.94.38022741.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9790.40.7862.183.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2IIR1.95075099397798.420.19170.189920.22459RANDOM36.551
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]
-0.83-0.991.49-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.841
r_dihedral_angle_4_deg22.701
r_dihedral_angle_3_deg14.85
r_dihedral_angle_1_deg5.908
r_scangle_it3.904
r_scbond_it2.388
r_mcangle_it1.549
r_angle_refined_deg1.414
r_mcbond_it0.858
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.841
r_dihedral_angle_4_deg22.701
r_dihedral_angle_3_deg14.85
r_dihedral_angle_1_deg5.908
r_scangle_it3.904
r_scbond_it2.388
r_mcangle_it1.549
r_angle_refined_deg1.414
r_mcbond_it0.858
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5804
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms29

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling