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K166 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 model from CCP4 cloud
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2M MgCl2
0.1M Bis-Tris pH 5.5
25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.998 α = 90 b = 147.23 β = 103.72 c = 97.969 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 2023-07-08 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 2.9 49.38 99.81 0.992 8.03 7.1 46401
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 2.9 3.004 0.592
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 2.9 49.38 44050 2326 99.91 0.19965 0.19693 0.25205 0.2213 RANDOM 68.737
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] -1.49 -0.31 0.86 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.051 r_dihedral_angle_2_deg 11.585 r_long_range_B_refined 8.316 r_dihedral_angle_1_deg 6.852 r_mcangle_it 3.599 r_scbond_it 3.306 r_angle_refined_deg 2.249 r_mcbond_it 2.131 r_chiral_restr 0.141 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.051 r_dihedral_angle_2_deg 11.585 r_long_range_B_refined 8.316 r_dihedral_angle_1_deg 6.852 r_mcangle_it 3.599 r_scbond_it 3.306 r_angle_refined_deg 2.249 r_mcbond_it 2.131 r_chiral_restr 0.141 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15906 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing