6F3U

The crystal structure of Glycogen Phosphorylase in complex with 10h

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		native T-state of GPb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	10 mM BES buffer

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.595	α = 90
b = 128.595	β = 90
c = 116.648	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS PILATUS 6M-F		2017-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	91	100	0.213	9.1	14.5		50194

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.27	100		2.8	14.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	native T-state of GPb	2.2	90.93	47694	2438	99.98	0.14366	0.14221	0.17224	RANDOM	43.795

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]
1.01			1.01		-2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.261
r_dihedral_angle_4_deg	18.551
r_dihedral_angle_3_deg	13.532
r_long_range_B_refined	6.623
r_long_range_B_other	6.623
r_dihedral_angle_1_deg	5.984
r_scangle_other	5.137
r_scbond_it	3.215
r_scbond_other	3.215
r_mcangle_it	3.118
r_mcangle_other	3.118
r_mcbond_it	2.07
r_mcbond_other	2.069
r_angle_refined_deg	1.35
r_angle_other_deg	0.967
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	6589
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing