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The complex of Glycogen Phosphorylase with (-)-Epigallocatechin-3-gallate (EGCG) and glucose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P7D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.7 289 10 mM BES buffer
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.183 α = 90 b = 126.183 β = 90 c = 115.232 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 100 PIXEL DECTRIS PILATUS 6M 2022-03-14 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 2 126.18 99.97 0.99 27.4 9.3 63292
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 0.995 10.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2 85.24 60075 3142 99.97 0.15723 0.15509 0.1677 0.19729 0.208 RANDOM 28.704
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 r_dihedral_angle_2_deg 32.071 r_dihedral_angle_4_deg 19.585 r_dihedral_angle_3_deg 13.965 r_dihedral_angle_1_deg 6.766 r_long_range_B_refined 6.736 r_long_range_B_other 6.735 r_scangle_other 4.8 r_scbond_it 3.432 r_scbond_other 3.422 r_mcangle_it 3.178
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.071 r_dihedral_angle_4_deg 19.585 r_dihedral_angle_3_deg 13.965 r_dihedral_angle_1_deg 6.766 r_long_range_B_refined 6.736 r_long_range_B_other 6.735 r_scangle_other 4.8 r_scbond_it 3.432 r_scbond_other 3.422 r_mcangle_it 3.178 r_mcangle_other 3.178 r_mcbond_it 2.328 r_mcbond_other 2.328 r_angle_refined_deg 1.587 r_angle_other_deg 1.38 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6649 Nucleic Acid Atoms Solvent Atoms 821 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement REFMAC phasing Aimless data scaling XDS data reduction PDB_EXTRACT data extraction Coot model building