2PRJ | pdb_00002prj

Binding of N-acetyl-beta-D-glucopyranosylamine to Glycogen Phosphorylase B

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.7	289	GLYCOGEN PHOSPHORYLASE WAS CO-CRYSTALLISED WITH 20 MM N-ACETYL-BETA-D-GLUCOPYRANOSYLAMINE IN A MEDIUM CONSISTING OF 20-30 MG/ML ENZYME, 1 MM IMP, 1 MM SPERMINE, 10 MM BES, 3 MM DITHIOTHREITOL, 0.1 MM EDTA, 0.02% (W/V) SODIUM AZIDE, PH 6.7 AT 16 C, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.47	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.5	α = 90
b = 128.5	β = 90
c = 116.3	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	298		SIEMENS		1994-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	SIEMENS

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	2.3	28.17	81.6	0.055	11.5	4		35730

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	2.3	2.4	46.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.3	18.17	35730	35730		81.6	0.181	0.181	0.237	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]

RMS Deviations
Key	Refinement Restraint Deviation
x_dihedral_angle_d	25.4
x_angle_deg	1.4
x_improper_angle_d	0.7
x_bond_d	0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6749
Nucleic Acid Atoms
Solvent Atoms	259
Heterogen Atoms	53

Software

Software
Software Name	Purpose
X-PLOR	refinement
XDS	data reduction
XDS	data scaling