6S4K

The crystal structure of glycogen phosphorylase in complex with 12


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910 mM BES buffer, pH 6.7
Crystal Properties
Matthews coefficientSolvent content
2.5451.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.165α = 90
b = 128.165β = 90
c = 115.879γ = 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
12.4313.52900.0760.99716.55.932703
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)
12.432.5378.60.4190.9013.14.3

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 SYNTHESISTHROUGHOUT2.4313.5231039159588.370.154540.151640.21106RANDOM27.161
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]
0.180.18-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.535
r_dihedral_angle_4_deg19.778
r_dihedral_angle_3_deg15.647
r_dihedral_angle_1_deg7.035
r_long_range_B_refined3.914
r_long_range_B_other3.903
r_scangle_other2.489
r_mcangle_it1.956
r_mcangle_other1.956
r_angle_refined_deg1.517
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.535
r_dihedral_angle_4_deg19.778
r_dihedral_angle_3_deg15.647
r_dihedral_angle_1_deg7.035
r_long_range_B_refined3.914
r_long_range_B_other3.903
r_scangle_other2.489
r_mcangle_it1.956
r_mcangle_other1.956
r_angle_refined_deg1.517
r_scbond_it1.46
r_scbond_other1.459
r_angle_other_deg1.297
r_mcbond_other1.144
r_mcbond_it1.143
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 Atoms6589
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
REFMACphasing