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Pyruvate Kinase Isoform L-type with phosphorylated Ser113 (pS113) in complex with FBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IP7 PDB entry 4IP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 0.1 M HEPES, pH 7.5, 10% ethylene glycol, 12% PEG8000
Crystal Properties Matthews coefficient Solvent content 2.92 57.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.774 α = 90 b = 111.843 β = 90 c = 127.507 γ = 90
Symmetry Space Group P 21 21 2
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 PILATUS3 6M 2017-01-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9778 SSRF BL18U1
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 2.36 48.59 97.9 0.147 0.162 0.066 0.994 7.8 6.2 56712
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 2.36 2.43 92 1.2 1.302 0.5 0.75 6.6
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4IP7 2.36 48.59 53862 2815 97.56 0.207 0.2035 0.2094 0.275 0.2767 RANDOM 59.669
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] -4.53 2.58 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.565 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 19.257 r_dihedral_angle_1_deg 7.167 r_angle_refined_deg 1.56 r_angle_other_deg 0.902 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.565 r_dihedral_angle_4_deg 19.954 r_dihedral_angle_3_deg 19.257 r_dihedral_angle_1_deg 7.167 r_angle_refined_deg 1.56 r_angle_other_deg 0.902 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8083 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 117
Software Software Software Name Purpose HKL-2000 data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction