2PYD

The crystal structure of Glycogen phosphorylase in complex with glucose at 100 K

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	10 MM BES BUFFER, 0.1 MM EDTA,0.02% NAN3, 3 MM DTT, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.73	α = 90
b = 125.73	β = 90
c = 114.933	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	100	CCD	MAR CCD 165 mm		2005-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8068	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.93	30	99.62	0.07	18.2	4.9	69442	65895		-3	19.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.93	1.96	99.8		0.432	4.2	4.9	3446

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	pdb entry 1WW2	1.93	30	69442	65895	3511	99.62	0.1926	0.1904	0.235	RANDOM	20.205

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]
0.74			0.74		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.878
r_dihedral_angle_4_deg	17.018
r_dihedral_angle_3_deg	12.915
r_dihedral_angle_1_deg	5.299
r_scangle_it	1.521
r_angle_refined_deg	1.103
r_scbond_it	0.935
r_mcangle_it	0.661
r_mcbond_it	0.392
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.878
r_dihedral_angle_4_deg	17.018
r_dihedral_angle_3_deg	12.915
r_dihedral_angle_1_deg	5.299
r_scangle_it	1.521
r_angle_refined_deg	1.103
r_scbond_it	0.935
r_mcangle_it	0.661
r_mcbond_it	0.392
r_nbtor_refined	0.304
r_nbd_refined	0.184
r_symmetry_vdw_refined	0.162
r_symmetry_hbond_refined	0.143
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6594
Nucleic Acid Atoms
Solvent Atoms	960
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.