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Structure of liver pyruvate kinase in complex with allosteric modulator 42
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QDN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 100 mM HEPES/MOPS, 10% PEG8000, 20% ethylene glycol, 10 mM phenylalanine, 20 mM sodium oxalate
Crystal Properties Matthews coefficient Solvent content 2.9 57.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.159 α = 90 b = 113.004 β = 91.14 c = 189.435 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER2 XE 16M 2021-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91788 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.855 104.559 94.8 0.081 0.049 0.999 9.8 3.7 282026
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.855 2.031 62.8 0.827 0.498 0.624 1.6 3.7
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.855 104.56 282026 14054 75.9 0.1996 0.1984 0.2221 0.2035 RANDOM 37.09
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] 0.7034 -0.6415 -0.1966 -0.5068
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.69 t_omega_torsion 3.07 t_angle_deg 0.87 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.69 t_omega_torsion 3.07 t_angle_deg 0.87 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25843 Nucleic Acid Atoms Solvent Atoms 2859 Heterogen Atoms 328
Software Software Software Name Purpose XDS data reduction PHASER phasing BUSTER refinement PDB_EXTRACT data extraction STARANISO data scaling