3KTX

Crystal structure of Leishmania mexicana pyruvate kinase (LmPYK)in complex with 1,3,6,8-pyrenetetrasulfonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PKLPDB entry 1PKL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.227712-16 % Peg 8,000, 20 mM triethanolamine-HCl buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0259.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.86α = 90
b = 129.86β = 90
c = 165.2γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2008-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.0ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.120.6999.90.0760.0820.1976957769572.12.131.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.211000.5270.5614.28.711124

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1PKL2.120.692.12.1769567309138651000.188210.185540.2388RANDOM44.681
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]
0.372.39-2.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.93
r_dihedral_angle_4_deg20.132
r_dihedral_angle_3_deg16.42
r_dihedral_angle_1_deg6.333
r_scangle_it5.393
r_scbond_it3.303
r_mcangle_it2.008
r_angle_refined_deg1.822
r_mcbond_it1.156
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.93
r_dihedral_angle_4_deg20.132
r_dihedral_angle_3_deg16.42
r_dihedral_angle_1_deg6.333
r_scangle_it5.393
r_scbond_it3.303
r_mcangle_it2.008
r_angle_refined_deg1.822
r_mcbond_it1.156
r_chiral_restr0.145
r_bond_refined_d0.024
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7506
Nucleic Acid Atoms
Solvent Atoms640
Heterogen Atoms68

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling