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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 isomorphous pdb entry 3GQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 291 25% w/v PEG-3350, 0.1M ammonium sulfate, 0.1M Bis-Tris, 0.005M activator (from 0.1M stock solution in DMSO)., pH 6.5, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.882 α = 90 b = 152.564 β = 103.17 c = 93.036 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 RIGAKU SATURN A200 2010-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 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 1.95 40 99.8 0.08 10.7 3.6 158866
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 1.95 1.98 97.4 0.857 3 7719
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 isomorphous pdb entry 3GQY 1.95 26.714 158798 1914 99.682 0.219 0.219 0.262 0.2333 thin shells (sftools) 23.419
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] -0.709 -1.136 0.028 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.075 r_dihedral_angle_4_deg 15.671 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 5.71 r_scangle_it 3.245 r_scbond_it 2.045 r_angle_refined_deg 1.425 r_mcangle_it 1.284 r_angle_other_deg 0.906 r_mcbond_it 0.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.075 r_dihedral_angle_4_deg 15.671 r_dihedral_angle_3_deg 13.272 r_dihedral_angle_1_deg 5.71 r_scangle_it 3.245 r_scbond_it 2.045 r_angle_refined_deg 1.425 r_mcangle_it 1.284 r_angle_other_deg 0.906 r_mcbond_it 0.723 r_mcbond_other 0.18 r_chiral_restr 0.078 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15143 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 202
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection HKL-2000 data reduction HKL-2000 data scaling