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Crystal structure of human Glucose-6-phosphate isomerase with phosphoenol pyruvate ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 Protein buffer: 20 mM Tris pH 7.4, 30 mM NaCl, 20 mM PEP ligand.
Reservoir: 21% w/v PEG3500, 0.16 M CaCl2, and 0.058 M HEPES, pH 7.0
Co-crystallization with ligand:
Hanging drop: 1.5:0.5:1.5 ul - Protein (8 mg/ml):Seed stock:Reservoir.
Cryoprotectant = a mixture containing the mother liquor, 24% v/v glycerol, and 15-20 mM ligand.
Crystal Properties Matthews coefficient Solvent content 2.33 47.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.84 α = 90 b = 107.482 β = 90 c = 271.193 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 PIXEL DECTRIS EIGER X 16M 2023-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.987 MAX IV BioMAX
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 1.6 48.42 99.76 0.1929 0.2006 0.05442 0.999 9.89 13.5 310109 19.17
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 1.6 1.657 99.79 3.025 3.142 0.8441 0.671 1.49 13.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 48.42 1.33 309569 15554 99.77 0.1887 0.1869 0.1936 0.2235 0.23 26.32
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 7.6431 f_angle_d 1.3579 f_chiral_restr 0.0767 f_bond_d 0.0154 f_plane_restr 0.0148
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17727 Nucleic Acid Atoms Solvent Atoms 1141 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing