4KCT

Pyruvate kinase (PYK) from Trypanosoma brucei soaked with Oxaloacetate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.227715-20% PEG 8,000, 10-20% glycerol, 80 uM F26BP, 800 uM Ponceau S, 50 mM TEA buffer, 100 mM KCl, 50 mM MgCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3863.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.99α = 90
b = 108.17β = 90
c = 264.49γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9574.5999.61071121071123.63.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0697.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1.9568.343101756101756534999.60.154430.152930.18308RANDOM27.309
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]
0.03-0.070.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.716
r_dihedral_angle_4_deg16.252
r_dihedral_angle_3_deg15.405
r_dihedral_angle_1_deg6.826
r_angle_refined_deg1.093
r_chiral_restr0.097
r_gen_planes_refined0.016
r_bond_refined_d0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7596
Nucleic Acid Atoms
Solvent Atoms781
Heterogen Atoms74

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling