3SYR | pdb_00003syr

Glycogen phosphorylase b in complex with beta-D-glucopyranonucleoside 5-fluorouracil

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	SMALL TUBES	6.7	289	2mM INHIBITOR SOAKED WITH T-STATE NATIVE ENZYME CRYSTAL FOR 2 HRS, pH 6.7, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.556	α = 90
b = 128.556	β = 90
c = 116.282	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	AGILENT ATLAS CCD	mirror	2011-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION ENHANCE ULTRA	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	2.4	30	95.9	0.11	11.5	4.8	36858	34960		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	89.4		0.497	2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.4	13.63	36858	34960	1866	95.86	0.1778	0.1778	0.17568	0.1728	0.21718	0.213	RANDOM	23.248

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]
0.55			0.55		-1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.812
r_dihedral_angle_4_deg	21.605
r_dihedral_angle_3_deg	17.546
r_dihedral_angle_1_deg	5.828
r_scangle_it	3.546
r_scbond_it	2.046
r_mcangle_it	1.343
r_angle_refined_deg	1.342
r_mcbond_it	0.681
r_chiral_restr	0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.812
r_dihedral_angle_4_deg	21.605
r_dihedral_angle_3_deg	17.546
r_dihedral_angle_1_deg	5.828
r_scangle_it	3.546
r_scbond_it	2.046
r_mcangle_it	1.343
r_angle_refined_deg	1.342
r_mcbond_it	0.681
r_chiral_restr	0.11
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6577
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	20

Software

Software
Software Name	Purpose
CrysalisPro	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

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.