2E20

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A)


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, 45% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.56α = 90
b = 110.56β = 90
c = 66.612γ = 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 mirror2006-03-23MSINGLE 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
12.43099.20.07422.131.481875558.02
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)
2.42.4995.20.4133.051775

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 1X3M2.4301757494599.280.201940.199430.25193RANDOM38.022
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]
2.981.492.98-4.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.522
r_dihedral_angle_4_deg15.339
r_dihedral_angle_3_deg14.006
r_dihedral_angle_1_deg5.859
r_scangle_it1.613
r_angle_refined_deg1.145
r_scbond_it1.07
r_angle_other_deg0.88
r_mcangle_it0.781
r_mcbond_it0.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.522
r_dihedral_angle_4_deg15.339
r_dihedral_angle_3_deg14.006
r_dihedral_angle_1_deg5.859
r_scangle_it1.613
r_angle_refined_deg1.145
r_scbond_it1.07
r_angle_other_deg0.88
r_mcangle_it0.781
r_mcbond_it0.705
r_symmetry_vdw_other0.223
r_nbd_refined0.192
r_nbd_other0.185
r_nbtor_refined0.167
r_symmetry_vdw_refined0.143
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.125
r_nbtor_other0.084
r_mcbond_other0.075
r_xyhbond_nbd_other0.067
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling