2GM9 | pdb_00002gm9

Structure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole

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, HANGING DROP	6.7	289	1.1mM IMP 1.1mM Spermin 10mM BES 2.9mM DTT 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.781	α = 90
b = 126.781	β = 90
c = 115.144	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	Toroidal Zerodur mirror	2001-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.93	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	91.29	98.34			40113	39447		1

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	2.54	39.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	IN HOUSE MODEL	2.3	91.29	1	40113	39447	2093	98.34	0.18564	0.18564	0.18249	0.2	0.2451	0.26	RANDOM	29.819

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]
1.3			1.3		-2.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.39
r_dihedral_angle_4_deg	20.133
r_dihedral_angle_3_deg	18.051
r_dihedral_angle_1_deg	6.784
r_scangle_it	2.754
r_scbond_it	1.889
r_angle_refined_deg	1.566
r_mcangle_it	1.141
r_angle_other_deg	1.14
r_mcbond_it	0.957
r_symmetry_vdw_other	0.256
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.211
r_nbd_other	0.19
r_nbtor_refined	0.181
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.171
r_mcbond_other	0.165
r_chiral_restr	0.09
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6545
Nucleic Acid Atoms
Solvent Atoms	455
Heterogen Atoms	38

Software

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