4FWO

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.1 M Bis-Tris pH 6.0, 35% Pentaerythritol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6253.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.921α = 90
b = 110.921β = 90
c = 66.789γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMirror2008-04-04MSINGLE 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
12.95097.60.14262.64.610515
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)
12.9396.70.3073.71031

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 REPLACEMENTTHROUGHOUT2E1Y2.9501051250197.480.23080.22810.2871RANDOM44.3506
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]
2.921.462.92-4.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.49
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg15.243
r_dihedral_angle_1_deg4.647
r_angle_refined_deg0.955
r_scangle_it0.654
r_mcangle_it0.476
r_scbond_it0.384
r_mcbond_it0.262
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.49
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg15.243
r_dihedral_angle_1_deg4.647
r_angle_refined_deg0.955
r_scangle_it0.654
r_mcangle_it0.476
r_scbond_it0.384
r_mcbond_it0.262
r_chiral_restr0.06
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2949
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms36

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling