3PP7

Crystal structure of Leishmania mexicana pyruvate kinase in complex with the drug suramin, an inhibitor of glycolysis.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.22777 12 % PEG 8,000, 20 mM triethanolamine-HCl buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10% glycerol, EVAPORATION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0659.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.77α = 90
b = 129.48β = 90
c = 165.75γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2008-12-11MSINGLE 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
12.3549.57980.0580.024226.5545422.352.3544.2
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)
12.352.48980.3520.1464.56.57772

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1PKL2.3544.735453751776276198.010.193420.191440.23119RANDOM70.735
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]
0.040.15-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.595
r_dihedral_angle_4_deg17.9
r_dihedral_angle_3_deg15.684
r_dihedral_angle_1_deg5.443
r_scangle_it2.145
r_scbond_it1.235
r_angle_refined_deg1.124
r_mcangle_it0.848
r_mcbond_it0.439
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.595
r_dihedral_angle_4_deg17.9
r_dihedral_angle_3_deg15.684
r_dihedral_angle_1_deg5.443
r_scangle_it2.145
r_scbond_it1.235
r_angle_refined_deg1.124
r_mcangle_it0.848
r_mcbond_it0.439
r_chiral_restr0.078
r_bond_refined_d0.008
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 Atoms7519
Nucleic Acid Atoms
Solvent Atoms436
Heterogen Atoms89

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling