4XH1

Crystal structure of Salmonella typhimurium propionate kinase in complex with AMPPNP and propionate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.150.1 M Bis-Tris pH 6.5, polyethylene glycol 2000
Crystal Properties
Matthews coefficientSolvent content
2.856.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.61α = 90
b = 111.61β = 90
c = 66.65γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.976ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1232.22990.071177.43223331.469
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)
122.1198.50.50747.3

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 REPLACEMENTTHROUGHOUT2E1Y232.2230589163498.770.182270.179950.22615RANDOM34.912
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.667
r_dihedral_angle_4_deg22.41
r_dihedral_angle_3_deg14.613
r_long_range_B_refined7.424
r_long_range_B_other7.423
r_dihedral_angle_1_deg6.677
r_scangle_other6.006
r_mcangle_it4.533
r_mcangle_other4.533
r_scbond_it4.129
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.667
r_dihedral_angle_4_deg22.41
r_dihedral_angle_3_deg14.613
r_long_range_B_refined7.424
r_long_range_B_other7.423
r_dihedral_angle_1_deg6.677
r_scangle_other6.006
r_mcangle_it4.533
r_mcangle_other4.533
r_scbond_it4.129
r_scbond_other4.128
r_mcbond_it3.375
r_mcbond_other3.368
r_angle_refined_deg1.953
r_angle_other_deg0.909
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2923
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
Cootmodel building
iMOSFLMdata reduction