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The complex of Glycogen Phosphorylase with (-)-Epigallocatechin-3-gallate (EGCG).
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 pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.43 49.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.855 α = 90 b = 126.855 β = 90 c = 115.428 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 2021-11-30 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 2 126.86 100 0.994 12 10.9 64044
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 99.9 0.975 5.3 11.4
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 2 89.7 60713 3167 99.79 0.16608 0.16384 0.20838 0.2498 RANDOM 35.61
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 30.671 r_dihedral_angle_4_deg 18.592 r_dihedral_angle_3_deg 13.69 r_long_range_B_refined 7.331 r_long_range_B_other 7.331 r_dihedral_angle_1_deg 6.651 r_scangle_other 5.523 r_mcangle_it 3.922 r_mcangle_other 3.922 r_scbond_it 3.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.671 r_dihedral_angle_4_deg 18.592 r_dihedral_angle_3_deg 13.69 r_long_range_B_refined 7.331 r_long_range_B_other 7.331 r_dihedral_angle_1_deg 6.651 r_scangle_other 5.523 r_mcangle_it 3.922 r_mcangle_other 3.922 r_scbond_it 3.901 r_scbond_other 3.901 r_mcbond_it 2.914 r_mcbond_other 2.914 r_angle_refined_deg 1.543 r_angle_other_deg 1.35 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 606 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement REFMAC phasing Aimless data scaling XDS data reduction PDB_EXTRACT data extraction Coot model building REFMAC phasing