3IOL | pdb_00003iol

Crystal structure of Glucagon-Like Peptide-1 in complex with the extracellular domain of the Glucagon-Like Peptide-1 Receptor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C59	PDB entry 3C59 without ligand

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.9	291	0.1M N-(2-Acetamido) Iminodiacetic Acid (ADA), pH 6.9, 14 vol-% (+/-)-2-Methyl-2,4-pentanediol (MPD), 9mM n-decyl-beta-D-thiomaltoside, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2	38.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.67	α = 90
b = 42.67	β = 90
c = 95.09	γ = 90

Symmetry
Space Group	P 21 2 21

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		2008-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0	MAX II	I911-3

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	2.1	95	98	0.111	14	7	10585	10348			25.8

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	2.1	2.2	98		0.449	5.3	7	1132

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3C59 without ligand	2.1	28.53	8786	8357	429	97.85	0.18058	0.17816	0.19	0.22622	0.24	RANDOM	13.663

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]
2.61			-1.42		-1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.406
r_dihedral_angle_3_deg	14.042
r_dihedral_angle_4_deg	13.082
r_dihedral_angle_1_deg	6.462
r_scangle_it	4.717
r_scbond_it	2.859
r_mcangle_it	1.885
r_angle_refined_deg	1.681
r_angle_other_deg	1.072
r_mcbond_it	1.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.406
r_dihedral_angle_3_deg	14.042
r_dihedral_angle_4_deg	13.082
r_dihedral_angle_1_deg	6.462
r_scangle_it	4.717
r_scbond_it	2.859
r_mcangle_it	1.885
r_angle_refined_deg	1.681
r_angle_other_deg	1.072
r_mcbond_it	1.003
r_mcbond_other	0.263
r_chiral_restr	0.097
r_bond_refined_d	0.02
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1024
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	33

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	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.