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Pyruvate kinase M2 (PKM2) mutant in complex with phenylalanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FXJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 NaCl, Tris, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.142 α = 90 b = 69.399 β = 106.536 c = 168.818 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 110 CCD RAYONIX MX300HE 2018-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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 2.18 27.112 96 0.052 35.6 6.9 113714
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 2.18 2.236 0.456
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 2.18 27.112 109108 5537 95.718 0.2 0.1978 0.2014 0.2405 0.2401 47.204
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] 0.008 -0.007 -0.027 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.926 r_dihedral_angle_4_deg 20.306 r_dihedral_angle_3_deg 17.602 r_lrange_other 9.254 r_lrange_it 9.251 r_dihedral_angle_1_deg 6.991 r_scangle_it 6.89 r_scangle_other 6.89 r_mcangle_it 5.769 r_mcangle_other 5.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.926 r_dihedral_angle_4_deg 20.306 r_dihedral_angle_3_deg 17.602 r_lrange_other 9.254 r_lrange_it 9.251 r_dihedral_angle_1_deg 6.991 r_scangle_it 6.89 r_scangle_other 6.89 r_mcangle_it 5.769 r_mcangle_other 5.769 r_scbond_it 4.473 r_scbond_other 4.473 r_mcbond_it 3.871 r_mcbond_other 3.871 r_angle_refined_deg 1.384 r_angle_other_deg 1.217 r_symmetry_nbd_refined 0.323 r_nbd_other 0.218 r_nbd_refined 0.21 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.153 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.118 r_metal_ion_refined 0.115 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.012 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15417 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing