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K115 acetylated human muscle pyruvate kinase, isoform M2 (PKM2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Ensamble of models from CCP4 cloud
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 5% Tacsimate
0.1M Hepes pH 6.8
12.14% PEG MME 5000
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.536 α = 90 b = 154.783 β = 107.4 c = 100.7 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.17 81.64 99.79 0.973 12.9 7.1 125584
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.248 0.347
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.17 81.64 119349 6232 99.97 0.22505 0.22299 0.26503 0.2424 RANDOM 68.921
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] 2.23 -1.16 -1.84 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.235 r_dihedral_angle_2_deg 13.366 r_long_range_B_refined 6.957 r_long_range_B_other 6.955 r_dihedral_angle_1_deg 6.815 r_scangle_other 3.794 r_mcangle_it 3.174 r_mcangle_other 3.174 r_scbond_it 2.48 r_scbond_other 2.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.235 r_dihedral_angle_2_deg 13.366 r_long_range_B_refined 6.957 r_long_range_B_other 6.955 r_dihedral_angle_1_deg 6.815 r_scangle_other 3.794 r_mcangle_it 3.174 r_mcangle_other 3.174 r_scbond_it 2.48 r_scbond_other 2.48 r_angle_refined_deg 2.142 r_mcbond_it 1.959 r_mcbond_other 1.959 r_angle_other_deg 0.834 r_chiral_restr 0.109 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_dihedral_angle_4_deg 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 15640 Nucleic Acid Atoms Solvent Atoms 267 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing