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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 replacement with pdb entry 3GQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 20% PEG3350, 0.2M diammonium tartrate, 0.005M activator, 0.005M ADP, vapor diffusion, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.35 47.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.275 α = 90 b = 153.206 β = 102.91 c = 93.138 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 MARMOSAIC 225 mm CCD 2009-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97934 CLSI 08ID-1
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 1.6 50 96.3 0.059 10.2 3.6 283418
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) 1.6 1.66 75.2 0.707 2.5 22112
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT isomorphous replacement with pdb entry 3GQY 1.6 30 280370 2916 96.273 0.208 0.208 0.2122 0.231 0.2351 thin shells (sftools) 20.294
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] -0.546 -0.94 -0.011 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.875 r_dihedral_angle_4_deg 15.465 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 5.375 r_scangle_it 2.803 r_mcangle_it 2.239 r_scbond_it 1.802 r_mcbond_it 1.483 r_angle_refined_deg 1.348 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.875 r_dihedral_angle_4_deg 15.465 r_dihedral_angle_3_deg 11.864 r_dihedral_angle_1_deg 5.375 r_scangle_it 2.803 r_mcangle_it 2.239 r_scbond_it 1.802 r_mcbond_it 1.483 r_angle_refined_deg 1.348 r_angle_other_deg 0.889 r_mcbond_other 0.434 r_chiral_restr 0.079 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15294 Nucleic Acid Atoms Solvent Atoms 917 Heterogen Atoms 292
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling Coot model building MolProbity model building prodrg refinement