2E1Z

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M Bis-Tris pH 6.5, 17% (w/v) polyethylene glycol monomethyl ether 5000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5952.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.483α = 90
b = 110.483β = 90
c = 66.607γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU2005-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

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
11.985099.90.07324.4113.883295945.2
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)
1.982.051000.4942.194.93248

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 1X3M1.983029989159695.940.192070.190550.22092RANDOM25.577
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]
1.610.811.61-2.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.497
r_dihedral_angle_4_deg18.982
r_dihedral_angle_3_deg13.617
r_dihedral_angle_1_deg5.695
r_scangle_it2.35
r_scbond_it1.425
r_angle_refined_deg1.177
r_mcangle_it1.077
r_angle_other_deg0.89
r_mcbond_it0.639
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.497
r_dihedral_angle_4_deg18.982
r_dihedral_angle_3_deg13.617
r_dihedral_angle_1_deg5.695
r_scangle_it2.35
r_scbond_it1.425
r_angle_refined_deg1.177
r_mcangle_it1.077
r_angle_other_deg0.89
r_mcbond_it0.639
r_symmetry_vdw_other0.228
r_nbd_refined0.198
r_symmetry_vdw_refined0.194
r_nbd_other0.189
r_nbtor_refined0.169
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.12
r_mcbond_other0.1
r_nbtor_other0.082
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2955
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms57

Software

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