4XH4

Crystal structure of Salmonella typhimurium propionate kinase A88V mutant, 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, 30% pentaerythritol ethoxylate, 0.05 M ammonium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.7955.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.96α = 90
b = 110.96β = 90
c = 66.44γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-02-22MSINGLE 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
11.832.0396.90.04717.54.742396
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)
11.81.995.60.4812.74.4

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 REPLACEMENTTHROUGHOUT2E1Y1.832.0340234212996.430.186680.18470.22373RANDOM32.676
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_deg36.173
r_dihedral_angle_4_deg20.42
r_dihedral_angle_3_deg13.644
r_long_range_B_refined7.273
r_long_range_B_other7.272
r_dihedral_angle_1_deg6.604
r_scangle_other5.857
r_mcangle_it4.104
r_mcangle_other4.104
r_scbond_it4.051
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.173
r_dihedral_angle_4_deg20.42
r_dihedral_angle_3_deg13.644
r_long_range_B_refined7.273
r_long_range_B_other7.272
r_dihedral_angle_1_deg6.604
r_scangle_other5.857
r_mcangle_it4.104
r_mcangle_other4.104
r_scbond_it4.051
r_scbond_other4.05
r_mcbond_it3.055
r_mcbond_other3.054
r_angle_refined_deg1.978
r_angle_other_deg0.953
r_chiral_restr0.128
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.003
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 Atoms2928
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction