3CEJ | pdb_00003cej

Human glycogen phosphorylase (tense state) in complex with the allosteric inhibitor AVE2865

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5		VAPOR DIFFUSION, HANGING DROP, 7 mg/ml in 20 mM BES, 1 mM EDTA, 0.5 mM DTT, pH 6.5, 50 mM NBG, 2.5 mM AVF (AVE2865)

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.27	α = 90
b = 123.27	β = 90
c = 121.88	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.3	20	80.8				25212

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	3.3	19.47	25212	1257	81.21	0.181	0.176	0.1822	0.271	0.1897	RANDOM	56.085

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]
0.04	0.02		0.04		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.435
r_dihedral_angle_4_deg	20.061
r_dihedral_angle_3_deg	18.882
r_dihedral_angle_1_deg	6.005
r_angle_refined_deg	1.259
r_scangle_it	1.22
r_scbond_it	0.728
r_mcangle_it	0.644
r_mcbond_it	0.354
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.435
r_dihedral_angle_4_deg	20.061
r_dihedral_angle_3_deg	18.882
r_dihedral_angle_1_deg	6.005
r_angle_refined_deg	1.259
r_scangle_it	1.22
r_scbond_it	0.728
r_mcangle_it	0.644
r_mcbond_it	0.354
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.248
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.185
r_symmetry_hbond_refined	0.152
r_chiral_restr	0.081
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12830
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	124

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	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 R01GM157729.