3IS4

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 8000, 20mM triethanolamine-HCl buffer (pH 7.2), 50mM MgCl2, 100mM KCl, 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-ray100IMAGE PLATEMAR555 FLAT PANELmirrors2008-11-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.98ESRFID23-1

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
12.120.6999.90.0760.02720.19769572.12.131.606
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)
2.12.211000.5270.1894.28.711124

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 1PKL2.120.692.12.17695673091386599.870.232140.23050.26321RANDOM37.446
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]
0.12.3-2.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.014
r_dihedral_angle_4_deg14.528
r_dihedral_angle_3_deg13.594
r_dihedral_angle_1_deg5.07
r_scangle_it2.098
r_scbond_it1.186
r_angle_refined_deg0.99
r_mcangle_it0.825
r_mcbond_it0.436
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.014
r_dihedral_angle_4_deg14.528
r_dihedral_angle_3_deg13.594
r_dihedral_angle_1_deg5.07
r_scangle_it2.098
r_scbond_it1.186
r_angle_refined_deg0.99
r_mcangle_it0.825
r_mcbond_it0.436
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7506
Nucleic Acid Atoms
Solvent Atoms643
Heterogen Atoms62

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling