2G9Q | pdb_00002g9q

The crystal structure of the glycogen phosphorylase b- 1AB complex

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	287	BES, EDTA, pH 6.7, SMALL TUBES, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.712	α = 90
b = 128.712	β = 90
c = 117.442	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	RIGAKU RAXIS IV	MSC/Yale double Mirrors	1999-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

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	2.5	24.69	91.3	0.069	10	3.7	31719	31719		-3	48.1

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)
	2.5	2.54	93.7		0.485	3.3	3.6	2352

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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1HLF	2.5	24.69	30080	30080	1613	91.45	0.19242	0.19242	0.18972	0.24276	RANDOM	53.861

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]
0.71			0.71		-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.581
r_dihedral_angle_4_deg	18.284
r_dihedral_angle_3_deg	17.733
r_dihedral_angle_1_deg	5.604
r_scangle_it	2.151
r_scbond_it	1.292
r_angle_refined_deg	1.199
r_mcangle_it	1.095
r_mcbond_it	0.613
r_nbtor_refined	0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.581
r_dihedral_angle_4_deg	18.284
r_dihedral_angle_3_deg	17.733
r_dihedral_angle_1_deg	5.604
r_scangle_it	2.151
r_scbond_it	1.292
r_angle_refined_deg	1.199
r_mcangle_it	1.095
r_mcbond_it	0.613
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.237
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.139
r_xyhbond_nbd_refined	0.136
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6553
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.