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Crystal structure of human pyruvate kinase M2 isoform
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1 M Tris, pH 7.5, 0.2 M NaCl, 14% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.763 α = 90 b = 152.573 β = 97.88 c = 94.405 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 CCD Bruker DIP-6040 2017-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 2.12 30 99.8 26.12 4.3 121473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.2
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 THROUGHOUT 2.12 29.96 114970 6128 99.54 0.19489 0.19194 0.25071 0.2689 RANDOM 33.386
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] 0.27 0.01 -0.13 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_4_deg 20.066 r_dihedral_angle_3_deg 17.925 r_long_range_B_refined 7.099 r_long_range_B_other 7.099 r_dihedral_angle_1_deg 6.927 r_scangle_other 4.992 r_mcangle_it 4.173 r_mcangle_other 4.173 r_scbond_it 3.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_4_deg 20.066 r_dihedral_angle_3_deg 17.925 r_long_range_B_refined 7.099 r_long_range_B_other 7.099 r_dihedral_angle_1_deg 6.927 r_scangle_other 4.992 r_mcangle_it 4.173 r_mcangle_other 4.173 r_scbond_it 3.16 r_scbond_other 3.16 r_mcbond_it 2.676 r_mcbond_other 2.676 r_angle_refined_deg 1.405 r_angle_other_deg 0.922 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 15947 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing