2GJ4

Structure of rabbit muscle glycogen phosphorylase in complex with ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		In house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	289	1.1mM IMP, 1.1mM Spermine, 0mM BES, 2.9mM DTT, 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.128	α = 90
b = 128.128	β = 90
c = 116.346	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	100	CCD	ADSC QUANTUM 4	Rh coated Si mirror	2001-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87	SRS	PX9.6

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	1.6	48.8	74.5	0.059	0.045	12	3.3	98023	94754		1

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	1.6	1.69	74.5		0.466	0.637	1.5	1.4	3556

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	In house model	1.6	48.8	1	127198	86732	4629	71.82	0.1889	0.1869	0.22616	RANDOM	16.45

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]
0.79			0.79		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.628
r_dihedral_angle_4_deg	16.728
r_dihedral_angle_3_deg	13.395
r_dihedral_angle_1_deg	5.655
r_scangle_it	1.779
r_angle_other_deg	1.324
r_scbond_it	1.241
r_angle_refined_deg	1.184
r_mcangle_it	0.756
r_mcbond_it	0.692
r_symmetry_vdw_other	0.243
r_nbd_refined	0.206
r_nbtor_refined	0.172
r_nbd_other	0.167
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.151
r_symmetry_hbond_refined	0.114
r_mcbond_other	0.103
r_symmetry_vdw_refined	0.083
r_nbtor_other	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6532
Nucleic Acid Atoms
Solvent Atoms	747
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
AMoRE	phasing