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Crystal Structure of PKM2 mutant L144P
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 7 291 0.2 M Sodium chloride, 0.1 M HEPES pH7.0, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.32 47.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.4 α = 90 b = 151.769 β = 100.59 c = 89.85 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 2022-08-24 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.6 44.16 98 0.095 0.109 0.054 0.997 9 4.1 63685
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.66 100 0.847 0.97 0.469 0.77 4.2
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 MOLECULAR REPLACEMENT THROUGHOUT 3GR4 2.6 42.01 60264 3197 97.6 0.26455 0.26295 0.29473 0.29 RANDOM 68.345
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] -2.82 -2.35 -1.77 5.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.143 r_long_range_B_refined 10.473 r_dihedral_angle_2_deg 9.537 r_dihedral_angle_1_deg 5.543 r_mcangle_it 3.626 r_scbond_it 2.839 r_mcbond_it 2.238 r_angle_refined_deg 1.425 r_chiral_restr 0.1 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.143 r_long_range_B_refined 10.473 r_dihedral_angle_2_deg 9.537 r_dihedral_angle_1_deg 5.543 r_mcangle_it 3.626 r_scbond_it 2.839 r_mcbond_it 2.238 r_angle_refined_deg 1.425 r_chiral_restr 0.1 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15411 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 116
Software Software Software Name Purpose XDS data reduction PHENIX refinement Aimless data scaling PHASER phasing Coot model building