2F3S | pdb_00002f3s

Crystal Structure of the glycogen phosphorylase B / ethyl-N-(beta-D-glucopyranosyl)oxamate complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRJ	pdb entry 2PRj

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.304	α = 90
b = 128.304	β = 90
c = 116.044	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	ADSC QUANTUM 4		2005-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8034	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	1.96	30	98.5	0.042	20.6	4.2	68828	68828		-3	28.2

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	1.96	1.99	98.1		0.443	3.8	4.2	3392

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 2PRj	1.96	30	68795	68795	3501	98.5	0.188	0.185	0.2131	RANDOM

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]
-3.316			-3.316		6.632

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.7
c_angle_deg	1.21
c_improper_angle_d	0.81
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6589
Nucleic Acid Atoms
Solvent Atoms	317
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

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.