3E3L

The R-state Glycogen Phosphorylase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9GPB	pdb entry 9gpb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	7.5	289	1.1-1.3 M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.895	α = 90
b = 189.92	β = 109.27
c = 88.16	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD		2008-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.97976	SRS	PX10.1

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	2.59	30	99.6	0.064	11.7	3.4	112937	107281		-3

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	2.6	2.64	99.6		0.358	3.89	3.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 9gpb	2.59	29.59	107281	107281	5654	99.29	0.20958	0.20656	0.26577	RANDOM	49.826

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]
-1.95		-0.36			1.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.841
r_dihedral_angle_3_deg	21.501
r_dihedral_angle_4_deg	19.187
r_dihedral_angle_1_deg	6.261
r_scangle_it	1.889
r_angle_refined_deg	1.341
r_scbond_it	1.125
r_mcangle_it	0.851
r_mcbond_it	0.471
r_nbtor_refined	0.312
r_nbd_refined	0.224
r_symmetry_vdw_refined	0.191
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.133
r_chiral_restr	0.096
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26363
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing