6F3J

The crystal structure of Glycogen Phosphorylase in complex with 10a


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthernative T-state of GPb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910 mM BES buffer
Crystal Properties
Matthews coefficientSolvent content
2.4750.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.539α = 90
b = 128.539β = 90
c = 116.455γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS 6M-F2017-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.212899.80.22910.310.649885
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2799.75.59.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTnative T-state of GPb2.290.8947423242599.650.137770.136280.16686RANDOM33.902
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]
1.611.61-3.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.231
r_dihedral_angle_4_deg19.051
r_dihedral_angle_3_deg12.825
r_long_range_B_refined7.435
r_long_range_B_other7.434
r_dihedral_angle_1_deg5.863
r_scangle_other5.714
r_scbond_it3.703
r_scbond_other3.702
r_mcangle_it3.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.231
r_dihedral_angle_4_deg19.051
r_dihedral_angle_3_deg12.825
r_long_range_B_refined7.435
r_long_range_B_other7.434
r_dihedral_angle_1_deg5.863
r_scangle_other5.714
r_scbond_it3.703
r_scbond_other3.702
r_mcangle_it3.305
r_mcangle_other3.305
r_mcbond_it2.227
r_mcbond_other2.223
r_angle_refined_deg1.264
r_angle_other_deg0.937
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms276
Heterogen Atoms69

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing