3CUW | pdb_00003cuw

Crystal structure of glycogen phosphorylase b in complex with N-(-D-glucopyranosyl)-N'-(2-naphthyl)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
2.46	49.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.418	α = 90
b = 128.418	β = 90
c = 116.353	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	MAR CCD 165 mm		2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8063	EMBL/DESY, HAMBURG	X13

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	30	99.5	0.056	17.1	5.3	65843	65843		-3	28.7

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	2.03	99.4		0.465	5.1	5.3

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1HLF	2	21.26	65793	62455	3338	99.5	0.19282	0.19156	0.19	0.21649	0.21	RANDOM	31.069

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]
0.65			0.65		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.076
r_dihedral_angle_4_deg	20.371
r_dihedral_angle_3_deg	15.08
r_dihedral_angle_1_deg	5.089
r_scangle_it	1.958
r_scbond_it	1.218
r_angle_refined_deg	1.031
r_mcangle_it	0.943
r_mcbond_it	0.552
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.076
r_dihedral_angle_4_deg	20.371
r_dihedral_angle_3_deg	15.08
r_dihedral_angle_1_deg	5.089
r_scangle_it	1.958
r_scbond_it	1.218
r_angle_refined_deg	1.031
r_mcangle_it	0.943
r_mcbond_it	0.552
r_nbtor_refined	0.304
r_nbd_refined	0.182
r_symmetry_vdw_refined	0.15
r_symmetry_hbond_refined	0.132
r_xyhbond_nbd_refined	0.103
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	6637
Nucleic Acid Atoms
Solvent Atoms	255
Heterogen Atoms	46

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 R01GM157729.