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Crystal Structure of PKM2 mutant R516C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GR4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 0.2 M Sodium chloride, 0.1 M Tris pH8.0, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.45 49.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.4 α = 90 b = 138.512 β = 90 c = 155.614 γ = 90
Symmetry Space Group P 21 21 21
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 2022-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.9789 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.5 49.92 100 0.999 17.1 12.1 79439 45.09
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.55 0.934
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3GR4 2.5 49.92 1.33 77910 3937 98.14 0.2394 0.2373 0.2373 0.2787 0.2787 56.19
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.154 f_angle_d 0.5483 f_chiral_restr 0.045 f_plane_restr 0.004 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15024 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 169
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling Coot model building PHASER phasing