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Crystal structure of PKM2 in complex with a natural activator
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 277 Sodium tartrate, potassium chloride, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.824 α = 90 b = 130.288 β = 93.969 c = 104.456 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 ADSC QUANTUM 315r 2017-07-11 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) R Merge I (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 2.7 30 98.4 0.11 11.8 4.1 54936
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 2.7 2.8 0.495
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.7 30 48066 2395 87.141 0.256 0.2557 0.2567 0.264 0.2662 44.423
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] 0.743 0.403 -0.437 -0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.64 r_dihedral_angle_3_deg 18.741 r_dihedral_angle_4_deg 13.769 r_lrange_it 7.355 r_lrange_other 7.355 r_mcangle_it 4.926 r_mcangle_other 4.926 r_dihedral_angle_1_deg 4.176 r_scangle_it 4.021 r_scangle_other 4.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.64 r_dihedral_angle_3_deg 18.741 r_dihedral_angle_4_deg 13.769 r_lrange_it 7.355 r_lrange_other 7.355 r_mcangle_it 4.926 r_mcangle_other 4.926 r_dihedral_angle_1_deg 4.176 r_scangle_it 4.021 r_scangle_other 4.02 r_mcbond_it 2.929 r_mcbond_other 2.928 r_scbond_it 2.344 r_scbond_other 2.343 r_angle_other_deg 2.337 r_angle_refined_deg 1.557 r_nbd_other 0.421 r_symmetry_nbd_refined 0.338 r_symmetry_xyhbond_nbd_refined 0.317 r_symmetry_nbd_other 0.247 r_xyhbond_nbd_other 0.224 r_nbd_refined 0.191 r_nbtor_refined 0.178 r_chiral_restr 0.13 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.077 r_symmetry_xyhbond_nbd_other 0.07 r_bond_other_d 0.035 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15630 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing