4FWK

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with AMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E1YPDB ENTRY 2E1Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.1M Bis-Tris pH 6.0, 30% hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.419α = 90
b = 111.419β = 90
c = 66.732γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirror2009-01-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.85099.50.11811.86.212025
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)
12.82.995.90.58551128

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 2E1Y2.8501202557599.450.23360.23120.2824RANDOM46.9403
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]
1.80.91.8-2.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.758
r_dihedral_angle_4_deg16.009
r_dihedral_angle_3_deg14.01
r_dihedral_angle_1_deg4.348
r_angle_refined_deg0.893
r_scangle_it0.494
r_mcangle_it0.424
r_scbond_it0.269
r_mcbond_it0.233
r_chiral_restr0.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.758
r_dihedral_angle_4_deg16.009
r_dihedral_angle_3_deg14.01
r_dihedral_angle_1_deg4.348
r_angle_refined_deg0.893
r_scangle_it0.494
r_mcangle_it0.424
r_scbond_it0.269
r_mcbond_it0.233
r_chiral_restr0.054
r_bond_refined_d0.005
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2922
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing