6S4O

The crystal structure of glycogen phosphorylase in complex with 9


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910 mM BES buffer, pH 6.7
Crystal Properties
Matthews coefficientSolvent content
2.5551.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.207α = 90
b = 128.207β = 90
c = 115.941γ = 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
12.3513.793.20.0780.99413.75.337798
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)
12.352.4480.90.4560.9072.43.7

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 SYNTHESISTHROUGHOUT2.3513.735896183992.480.155280.152660.20741RANDOM26.907
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]
0.110.11-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.717
r_dihedral_angle_4_deg19.324
r_dihedral_angle_3_deg15.577
r_dihedral_angle_1_deg6.902
r_long_range_B_refined5.859
r_long_range_B_other5.856
r_scangle_other4.476
r_scbond_it2.819
r_scbond_other2.819
r_mcangle_it2.729
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.717
r_dihedral_angle_4_deg19.324
r_dihedral_angle_3_deg15.577
r_dihedral_angle_1_deg6.902
r_long_range_B_refined5.859
r_long_range_B_other5.856
r_scangle_other4.476
r_scbond_it2.819
r_scbond_other2.819
r_mcangle_it2.729
r_mcangle_other2.729
r_mcbond_it1.725
r_mcbond_other1.722
r_angle_refined_deg1.458
r_angle_other_deg1.277
r_chiral_restr0.071
r_bond_refined_d0.008
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 Atoms244
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing