2E1Y

Crystal structure of propionate kinase (TdcD) from Salmonella typhimurium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1X3MPDB entry 1X3M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch method6.52930.1 Bis-Tris pH 6.5, 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), Microbatch method, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.811α = 90
b = 110.811β = 90
c = 66.533γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirror2005-11-29MSINGLE 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
12.63098.30.1019.733.561481857.3
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)
2.62.6984.30.452.21235

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1X3M2.6301341570695.520.20220.199660.25311RANDOM34.052
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]
2.11.052.1-3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.526
r_dihedral_angle_4_deg19.877
r_dihedral_angle_3_deg13.691
r_dihedral_angle_1_deg5.554
r_scangle_it1.199
r_angle_refined_deg0.932
r_angle_other_deg0.809
r_mcangle_it0.697
r_scbond_it0.685
r_mcbond_it0.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.526
r_dihedral_angle_4_deg19.877
r_dihedral_angle_3_deg13.691
r_dihedral_angle_1_deg5.554
r_scangle_it1.199
r_angle_refined_deg0.932
r_angle_other_deg0.809
r_mcangle_it0.697
r_scbond_it0.685
r_mcbond_it0.387
r_nbd_refined0.198
r_symmetry_vdw_other0.19
r_nbd_other0.178
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.142
r_symmetry_hbond_refined0.116
r_symmetry_vdw_refined0.111
r_nbtor_other0.081
r_chiral_restr0.054
r_mcbond_other0.041
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2944
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling