4FWP

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M Bis-Tris pH 6.5, 30% hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6553.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.489α = 90
b = 111.489β = 90
c = 66.888γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirror2008-11-20MSINGLE 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
12.55099.80.08819.315.716944
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)
12.52.5999.90.47112.91682

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 REPLACEMENTTHROUGHOUT2E1Y2.5501691785799.570.23690.23540.2661RANDOM54.7753
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]
2.511.252.51-3.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_dihedral_angle_4_deg17.881
r_dihedral_angle_3_deg13.961
r_dihedral_angle_1_deg4.607
r_angle_refined_deg0.922
r_scangle_it0.872
r_mcangle_it0.526
r_scbond_it0.482
r_mcbond_it0.286
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.757
r_dihedral_angle_4_deg17.881
r_dihedral_angle_3_deg13.961
r_dihedral_angle_1_deg4.607
r_angle_refined_deg0.922
r_scangle_it0.872
r_mcangle_it0.526
r_scbond_it0.482
r_mcbond_it0.286
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2926
Nucleic Acid Atoms
Solvent Atoms67
Heterogen Atoms36

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling