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Activator-Bound Structure of Human Pyruvate Kinase M2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GQY Direct placement of PDB entry 3GQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 291 25% PEG3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 0.005M activator, pH 5.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.343 α = 90 b = 155.69 β = 108.04 c = 101.789 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 IMAGE PLATE RIGAKU RAXIS 2009-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E DW 1.5418
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 20 97 0.077 11.2 3.6 157058
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 2.07 96.8 0.947 3.6 15625
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Direct placement of PDB entry 3GQY 2 19.96 152479 1859 94.23 0.248 0.247 0.287 0.2792 thin shells (SFTOOLS) 33.749
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] -1.396 -2.3 1.67 -1.698
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 32.837 f_dihedral_angle_4_deg 16.519 f_dihedral_angle_3_deg 13.054 f_dihedral_angle_1_deg 5.402 f_mcangle_it 1.542 f_scangle_it 1.457 f_angle_refined_deg 1.162 f_mcbond_it 1.073 f_scbond_it 1.025 f_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_2_deg 32.837 f_dihedral_angle_4_deg 16.519 f_dihedral_angle_3_deg 13.054 f_dihedral_angle_1_deg 5.402 f_mcangle_it 1.542 f_scangle_it 1.457 f_angle_refined_deg 1.162 f_mcbond_it 1.073 f_scbond_it 1.025 f_angle_other_deg 0.862 f_mcbond_other 0.273 f_symmetry_vdw_other 0.265 f_nbd_refined 0.189 f_nbd_other 0.186 f_symmetry_hbond_refined 0.184 f_nbtor_refined 0.164 f_xyhbond_nbd_refined 0.129 f_nbtor_other 0.081 f_chiral_restr 0.062 f_symmetry_vdw_refined 0.021 f_bond_refined_d 0.012 f_gen_planes_refined 0.003 f_bond_other_d 0.002 f_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14722 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms 157
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling