9HIA | pdb_00009hia

K115 acetylated human muscle pyruvate kinase, isoform M2 (PKM2), in complex with FBP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherEnsamble of models created with CCP4 cloud

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2985% Tacsimate, 0.1M Hepes pH 6.8 13.57% PEG MME 5000
Crystal Properties
Matthews coefficientSolvent content
2.5852.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.229α = 90
b = 155.169β = 107.61
c = 101.023γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.0229.6998.050.99918.567.21527002.02
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.022.0920.863

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.0229.69145134759498.080.161890.159830.16060.200450.2023RANDOM36.088
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]
1.5-2.52-0.530.52
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined16.346
r_dihedral_angle_3_deg14.959
r_dihedral_angle_2_deg10.641
r_dihedral_angle_1_deg6.29
r_rigid_bond_restr5.382
r_mcangle_it4.766
r_scbond_it3.844
r_mcbond_it2.961
r_angle_refined_deg2.311
r_chiral_restr0.173
RMS Deviations
KeyRefinement Restraint Deviation
r_long_range_B_refined16.346
r_dihedral_angle_3_deg14.959
r_dihedral_angle_2_deg10.641
r_dihedral_angle_1_deg6.29
r_rigid_bond_restr5.382
r_mcangle_it4.766
r_scbond_it3.844
r_mcbond_it2.961
r_angle_refined_deg2.311
r_chiral_restr0.173
r_bond_refined_d0.015
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15888
Nucleic Acid Atoms
Solvent Atoms1419
Heterogen Atoms154

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing