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The crystal structure of glycogen phosphorylase in complex with baicalein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.8 289 10 mM BES buffer
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.51 α = 90 b = 128.51 β = 90 c = 116.59 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 IMAGE PLATE MAR scanner 345 mm plate 2020-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.25 51.6 97.5 0.132 0.984 6.3 3.8 45448
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 2.25 2.32 0.669
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 6R0H 2.25 51.6 43182 2243 96.98 0.15357 0.15104 0.1513 0.20261 0.2029 RANDOM 40.704
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] 0.14 0.14 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.55 r_dihedral_angle_4_deg 21.444 r_dihedral_angle_3_deg 16.543 r_long_range_B_refined 7.417 r_dihedral_angle_1_deg 6.876 r_scbond_it 3.527 r_mcangle_it 3.372 r_mcbond_it 2.105 r_angle_refined_deg 1.815 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.55 r_dihedral_angle_4_deg 21.444 r_dihedral_angle_3_deg 16.543 r_long_range_B_refined 7.417 r_dihedral_angle_1_deg 6.876 r_scbond_it 3.527 r_mcangle_it 3.372 r_mcbond_it 2.105 r_angle_refined_deg 1.815 r_chiral_restr 0.126 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6589 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing