3G2L | pdb_00003g2l

Crystal structure of 1-(beta-D-glucopyranosyl)-4-substituted-1,2,3-triazoles in complex with glycogen phosphorylase

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	6.8	289	pH 6.8, SMALL TUBES, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.791	α = 90
b = 128.791	β = 90
c = 116.188	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	MARRESEARCH		2007-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.80880	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	30	99	0.091	19.9	5.3		43536			30.8

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)
	2.3	2.34	98.6		0.501	3.9	5.3	2120

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2PRJ	2.3	30	41320	2193	98.88	0.17612	0.17427	0.17	0.21049	0.21	RANDOM	27.978

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]
0.57			0.57		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.788
r_dihedral_angle_4_deg	19.253
r_dihedral_angle_3_deg	16.075
r_dihedral_angle_1_deg	5.401
r_scangle_it	2.099
r_scbond_it	1.254
r_angle_refined_deg	1.085
r_mcangle_it	0.953
r_mcbond_it	0.534
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.788
r_dihedral_angle_4_deg	19.253
r_dihedral_angle_3_deg	16.075
r_dihedral_angle_1_deg	5.401
r_scangle_it	2.099
r_scbond_it	1.254
r_angle_refined_deg	1.085
r_mcangle_it	0.953
r_mcbond_it	0.534
r_nbtor_refined	0.302
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.147
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.081
r_symmetry_hbond_refined	0.057
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6604
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	26

Software

Software
Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.