8QMU

The complex of Glycogen Phosphorylase with (-)-Epigallocatechin-3-gallate (EGCG).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7P7D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.728910 mM BES pH 6.7
Crystal Properties
Matthews coefficientSolvent content
2.4349.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.855α = 90
b = 126.855β = 90
c = 115.428γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9763PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12126.861000.9941210.964044
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0599.90.9755.311.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT289.760713316799.790.166080.163840.20838RANDOM35.61
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.671
r_dihedral_angle_4_deg18.592
r_dihedral_angle_3_deg13.69
r_long_range_B_refined7.331
r_long_range_B_other7.331
r_dihedral_angle_1_deg6.651
r_scangle_other5.523
r_mcangle_it3.922
r_mcangle_other3.922
r_scbond_it3.901
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.671
r_dihedral_angle_4_deg18.592
r_dihedral_angle_3_deg13.69
r_long_range_B_refined7.331
r_long_range_B_other7.331
r_dihedral_angle_1_deg6.651
r_scangle_other5.523
r_mcangle_it3.922
r_mcangle_other3.922
r_scbond_it3.901
r_scbond_other3.901
r_mcbond_it2.914
r_mcbond_other2.914
r_angle_refined_deg1.543
r_angle_other_deg1.35
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms6649
Nucleic Acid Atoms
Solvent Atoms606
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
REFMACphasing
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
Cootmodel building
REFMACphasing