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Crystal structure of PKM2 R399E mutant complexed with FBP and serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 KCl, Tris, PEG3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.601 α = 90 b = 137.875 β = 90 c = 149.709 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.975 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.64 30 99.9 16.59 4.8 72242
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.64 2.73 100 0.491 4 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4B2D 2.64 30 67778 3614 99.86 0.18194 0.18 0.1856 0.21844 0.2045 RANDOM 43.372
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] 0.6 1.36 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.165 r_dihedral_angle_4_deg 18.899 r_dihedral_angle_3_deg 18.53 r_long_range_B_refined 8.715 r_long_range_B_other 8.715 r_scangle_other 6.766 r_dihedral_angle_1_deg 6.482 r_mcangle_it 5.085 r_mcangle_other 5.085 r_scbond_it 4.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.165 r_dihedral_angle_4_deg 18.899 r_dihedral_angle_3_deg 18.53 r_long_range_B_refined 8.715 r_long_range_B_other 8.715 r_scangle_other 6.766 r_dihedral_angle_1_deg 6.482 r_mcangle_it 5.085 r_mcangle_other 5.085 r_scbond_it 4.273 r_scbond_other 4.273 r_mcbond_it 3.335 r_mcbond_other 3.335 r_angle_refined_deg 1.477 r_angle_other_deg 0.75 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 15838 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing