3QV8

Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with benzothiazole-2,5-disulfonic acid.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22777-16% PEG 8,000, 20 mM TEA buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10-25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0459.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.554α = 90
b = 131.282β = 90
c = 167.602γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031DiamondI03

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
12.4544.411000.0950.10216.17.3360184491232.452.4552.1
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)
12.452.581000.5630.6054.17.57089

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 REPLACEMENTTHROUGHOUT1PKL2.4544.4146606248599.90.236080.234480.26576RANDOM52.196
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]
-1.133.92-2.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.004
r_dihedral_angle_4_deg16.723
r_dihedral_angle_3_deg16.33
r_dihedral_angle_1_deg5.672
r_scangle_it2.448
r_scbond_it1.401
r_angle_refined_deg1.259
r_mcangle_it1.019
r_mcbond_it0.536
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.004
r_dihedral_angle_4_deg16.723
r_dihedral_angle_3_deg16.33
r_dihedral_angle_1_deg5.672
r_scangle_it2.448
r_scbond_it1.401
r_angle_refined_deg1.259
r_mcangle_it1.019
r_mcbond_it0.536
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms6748
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms54

Software

Software
Software NamePurpose
DNAdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling