☰ Navigation Tabs
The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.8 289 10 mM BES buffer
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.607 α = 90 b = 128.607 β = 90 c = 116.633 γ = 90
Symmetry Space Group P 43 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 298 PIXEL DECTRIS PILATUS 6M 2019-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 86.4 99.9 0.998 15.1 6.5 128346 28.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 99.9 0.621 0.9
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 7O8E 1.6 64.39 121187 6459 99.37 0.13014 0.12851 0.1409 0.16112 0.1711 RANDOM 36.348
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] 0.61 0.61 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.163 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 5.68 r_long_range_B_refined 3.486 r_long_range_B_other 3.288 r_scangle_other 2.672 r_mcangle_it 2.175 r_mcangle_other 2.175 r_scbond_it 2.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.163 r_dihedral_angle_4_deg 18.452 r_dihedral_angle_3_deg 12.519 r_dihedral_angle_1_deg 5.68 r_long_range_B_refined 3.486 r_long_range_B_other 3.288 r_scangle_other 2.672 r_mcangle_it 2.175 r_mcangle_other 2.175 r_scbond_it 2.003 r_scbond_other 2.003 r_mcbond_it 1.612 r_mcbond_other 1.609 r_rigid_bond_restr 1.376 r_angle_refined_deg 1.218 r_angle_other_deg 1.13 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6589 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing