6S4P

The crystal structure of glycogen phosphorylase in complex with 13


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910 mM BES buffer, pH 6.7
Crystal Properties
Matthews coefficientSolvent content
2.5451.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.946α = 90
b = 127.946β = 90
c = 115.796γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDAGILENT ATLAS CCD2018-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION SUPERNOVA1.5419

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.3713.88900.0850.99612.65.135139
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.372.4677.20.5670.8552.13.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.3713.8833341176288.670.156780.153730.21354RANDOM29.555
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]
0.150.15-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.09
r_dihedral_angle_4_deg18.356
r_dihedral_angle_3_deg15.574
r_dihedral_angle_1_deg6.959
r_long_range_B_refined5.982
r_long_range_B_other5.972
r_scangle_other4.551
r_mcangle_it3.071
r_mcangle_other3.071
r_scbond_it2.871
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.09
r_dihedral_angle_4_deg18.356
r_dihedral_angle_3_deg15.574
r_dihedral_angle_1_deg6.959
r_long_range_B_refined5.982
r_long_range_B_other5.972
r_scangle_other4.551
r_mcangle_it3.071
r_mcangle_other3.071
r_scbond_it2.871
r_scbond_other2.871
r_mcbond_it1.991
r_mcbond_other1.99
r_angle_refined_deg1.506
r_angle_other_deg1.273
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms6582
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing