2QN3 | pdb_00002qn3

Glycogen Phosphorylase in complex with N-4-chlorobenzoyl-N-beta-D-glucopyranosyl urea

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRJ	pdb entry 2PRJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	10 mM Bes, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.841	α = 90
b = 128.841	β = 90
c = 116.486	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	CCD	ADSC QUANTUM 4		2006-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.912	SRS	PX9.6

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	1.95	99	97.9	0.046	20.1	5.2	70275	70275		-3	25

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)
	1.95	1.99	93.1		0.318	4.3	5.3	3280

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 2PRJ	1.96	91.29	66980	66980	3563	99.82	0.1858	0.18469	0.2064	RANDOM	27.235

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]
0.63			0.63		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.119
r_dihedral_angle_4_deg	19.562
r_dihedral_angle_3_deg	14.679
r_dihedral_angle_1_deg	5.096
r_scangle_it	1.931
r_scbond_it	1.205
r_angle_refined_deg	1.011
r_mcangle_it	0.901
r_mcbond_it	0.536
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.119
r_dihedral_angle_4_deg	19.562
r_dihedral_angle_3_deg	14.679
r_dihedral_angle_1_deg	5.096
r_scangle_it	1.931
r_scbond_it	1.205
r_angle_refined_deg	1.011
r_mcangle_it	0.901
r_mcbond_it	0.536
r_nbtor_refined	0.301
r_nbd_refined	0.175
r_symmetry_vdw_refined	0.139
r_symmetry_hbond_refined	0.116
r_xyhbond_nbd_refined	0.095
r_chiral_restr	0.073
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6632
Nucleic Acid Atoms
Solvent Atoms	332
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.