3FRO

Crystal structure of Pyrococcus abyssi glycogen synthase with open and closed conformations

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BIS	PDB ENTRY 2BIS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	26-30% MPD, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.998	α = 90
b = 139.913	β = 90
c = 159.414	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2008-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.5	25	99.7	0.078	0.099	8.4	3.9	58723	58364	2	2	55.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	97.6		0.41	0.32	1.1	3.7	1964

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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		THROUGHOUT	PDB ENTRY 2BIS	2.5	24.91	2	58527	58364	2950	99.39	0.288	0.216	0.214	0.255	RANDOM	43.416

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]
-0.26			0.92		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.785
r_dihedral_angle_3_deg	14.931
r_dihedral_angle_4_deg	13.818
r_dihedral_angle_1_deg	4.803
r_angle_refined_deg	0.825
r_angle_other_deg	0.74
r_scangle_it	0.494
r_scbond_it	0.322
r_mcangle_it	0.245
r_mcbond_it	0.223
r_nbtor_refined	0.173
r_nbd_other	0.168
r_nbd_refined	0.166
r_symmetry_vdw_other	0.124
r_symmetry_vdw_refined	0.113
r_symmetry_hbond_refined	0.101
r_xyhbond_nbd_refined	0.097
r_nbtor_other	0.08
r_chiral_restr	0.05
r_mcbond_other	0.021
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10452
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing