1P4G | pdb_00001p4g

Crystal structure of glycogen phosphorylase b in complex with C-(1-azido-alpha-D-glucopyranosyl)formamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GFZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	BES, EDTA, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.869	α = 90
b = 127.869	β = 90
c = 115.623	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	IMAGE PLATE	MARRESEARCH		2003-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8015	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	2.1	30	99.2	0.076	17.6	6.9	55927	55927		-3	28.6

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	2.1	2.14	99.3		0.519	2.1	5.8	2726

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	1GFZ	2.1	29.95	55898	55898	2825	99.1	0.183	0.183	0.204	RANDOM	33.4

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]
3.31			3.31		-6.63

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.4
c_scangle_it	3.46
c_scbond_it	2.27
c_mcangle_it	2.08
c_mcbond_it	1.31
c_angle_deg	1.3
c_improper_angle_d	0.78
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6585
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	32

Software

Software
Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
CNS	phasing