5X0I

Crystal structure of PKM2 R399E mutant complexed with FBP and serine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4B2D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP277KCl, Tris, PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.550.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.601α = 90
b = 137.875β = 90
c = 149.709γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13C10.975NSRRCBL13C1

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
12.643099.916.594.872242
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.642.731000.49145

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 REPLACEMENTTHROUGHOUT4B2D2.643067778361499.860.181940.180.21844RANDOM43.372
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]
0.61.36-1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.165
r_dihedral_angle_4_deg18.899
r_dihedral_angle_3_deg18.53
r_long_range_B_refined8.715
r_long_range_B_other8.715
r_scangle_other6.766
r_dihedral_angle_1_deg6.482
r_mcangle_it5.085
r_mcangle_other5.085
r_scbond_it4.273
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.165
r_dihedral_angle_4_deg18.899
r_dihedral_angle_3_deg18.53
r_long_range_B_refined8.715
r_long_range_B_other8.715
r_scangle_other6.766
r_dihedral_angle_1_deg6.482
r_mcangle_it5.085
r_mcangle_other5.085
r_scbond_it4.273
r_scbond_other4.273
r_mcbond_it3.335
r_mcbond_other3.335
r_angle_refined_deg1.477
r_angle_other_deg0.75
r_chiral_restr0.083
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15838
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing