3CUV

Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides

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, pH6.7, SMALL TUBES, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.45	α = 90
b = 126.45	β = 90
c = 115.465	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	MARMOSAIC 225 mm CCD		2006-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	1.488	SRS	PX14.1

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	1.93	30	99.9	0.094	11.6	6.2	70802	70802		-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)
	1.93	1.96	100		0.409	4.1	6.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1HLF	1.93	29.97	70733	67162	3571	99.83	0.19768	0.19592	0.23096	RANDOM	25.626

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			1		-2.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.52
r_dihedral_angle_4_deg	17.772
r_dihedral_angle_3_deg	12.835
r_dihedral_angle_1_deg	5.267
r_scangle_it	1.551
r_angle_refined_deg	0.989
r_scbond_it	0.972
r_mcangle_it	0.722
r_mcbond_it	0.432
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.52
r_dihedral_angle_4_deg	17.772
r_dihedral_angle_3_deg	12.835
r_dihedral_angle_1_deg	5.267
r_scangle_it	1.551
r_angle_refined_deg	0.989
r_scbond_it	0.972
r_mcangle_it	0.722
r_mcbond_it	0.432
r_nbtor_refined	0.302
r_symmetry_vdw_refined	0.181
r_nbd_refined	0.18
r_symmetry_hbond_refined	0.117
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6638
Nucleic Acid Atoms
Solvent Atoms	860
Heterogen Atoms	82

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
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 R01GM133198.