3S0J

The crystal structure of glycogen phosphorylase b in complex with 2,5-dihydroxy-4-(beta-D-glucopyranosyl)-chlorobenzene

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	10 mM BES Buffer, 3 mM DTT, 1 mM IMP, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.45	α = 90
b = 128.45	β = 90
c = 116.364	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	CCD	MAR CCD 165 mm		2005-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8156	EMBL/DESY, HAMBURG	X11

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	2	30	93.9	0.065	21.2	5.4	65452	64845		-3	31.1

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	2	2.03	90.9		0.398	5.2	5.4	3213

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2PRJ	2	30	65452	62101	3308	99	0.19105	0.19105	0.19005	0.20947	RANDOM	35.178

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]
0.93			0.93		-1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.526
r_dihedral_angle_4_deg	19.475
r_dihedral_angle_3_deg	15.234
r_dihedral_angle_1_deg	5.109
r_scangle_it	2.055
r_scbond_it	1.263
r_angle_refined_deg	1.028
r_mcangle_it	0.954
r_mcbond_it	0.56
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.526
r_dihedral_angle_4_deg	19.475
r_dihedral_angle_3_deg	15.234
r_dihedral_angle_1_deg	5.109
r_scangle_it	2.055
r_scbond_it	1.263
r_angle_refined_deg	1.028
r_mcangle_it	0.954
r_mcbond_it	0.56
r_nbtor_refined	0.302
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.098
r_chiral_restr	0.073
r_symmetry_hbond_refined	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6604
Nucleic Acid Atoms
Solvent Atoms	265
Heterogen Atoms	20

Software

Software
Software Name	Purpose
DNA	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.