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K115 acetylated human muscle pyruvate kinase, isoform M2 (PKM2), in complex with FBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Ensamble of models created with CCP4 cloud
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 5% Tacsimate,
0.1M Hepes pH 6.8
13.57% PEG MME 5000
Crystal Properties Matthews coefficient Solvent content 2.58 52.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.229 α = 90 b = 155.169 β = 107.61 c = 101.023 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 2.02 29.69 98.05 0.999 18.56 7.2 152700 2.02
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 2.02 2.092 0.863
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.02 29.69 145134 7594 98.08 0.16189 0.15983 0.1606 0.20045 0.2023 RANDOM 36.088
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 -0.53 0.52
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.346 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_2_deg 10.641 r_dihedral_angle_1_deg 6.29 r_rigid_bond_restr 5.382 r_mcangle_it 4.766 r_scbond_it 3.844 r_mcbond_it 2.961 r_angle_refined_deg 2.311 r_chiral_restr 0.173
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.346 r_dihedral_angle_3_deg 14.959 r_dihedral_angle_2_deg 10.641 r_dihedral_angle_1_deg 6.29 r_rigid_bond_restr 5.382 r_mcangle_it 4.766 r_scbond_it 3.844 r_mcbond_it 2.961 r_angle_refined_deg 2.311 r_chiral_restr 0.173 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 Atoms Number Protein Atoms 15888 Nucleic Acid Atoms Solvent Atoms 1419 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing