7ONF

The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7O8E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.828910 mM BES buffer
Crystal Properties
Matthews coefficientSolvent content
2.4850.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.607α = 90
b = 128.607β = 90
c = 116.633γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 6M2019-05-14MSINGLE 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
11.686.499.90.99815.16.512834628.2
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)RedundancyNumber Unique Reflections (All)
11.61.6399.90.6210.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT7O8E1.664.39121187645999.370.130140.128510.16112RANDOM36.348
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]
0.610.61-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.163
r_dihedral_angle_4_deg18.452
r_dihedral_angle_3_deg12.519
r_dihedral_angle_1_deg5.68
r_long_range_B_refined3.486
r_long_range_B_other3.288
r_scangle_other2.672
r_mcangle_it2.175
r_mcangle_other2.175
r_scbond_it2.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.163
r_dihedral_angle_4_deg18.452
r_dihedral_angle_3_deg12.519
r_dihedral_angle_1_deg5.68
r_long_range_B_refined3.486
r_long_range_B_other3.288
r_scangle_other2.672
r_mcangle_it2.175
r_mcangle_other2.175
r_scbond_it2.003
r_scbond_other2.003
r_mcbond_it1.612
r_mcbond_other1.609
r_rigid_bond_restr1.376
r_angle_refined_deg1.218
r_angle_other_deg1.13
r_chiral_restr0.081
r_bond_refined_d0.007
r_gen_planes_refined0.005
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6589
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing