4OO9 | pdb_00004oo9

Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator mavoglurant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EML	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19
experimental model	PDB	3UON	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19
experimental model	PDB	4DAJ	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19
experimental model	PDB	4DKL	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19
experimental model	PDB	4DJH	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19
experimental model	PDB	3V2Y	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19
experimental model	PDB	4EA3	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19
experimental model	PDB	1U19	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	6.8	293.1	24-34% v/v PEG400, 0.2 M ammonium phosphate dibasic, 0.1 M MES, pH 6.8, LIPIDIC CUBIC PHASE, temperature 293.1K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.242	α = 90
b = 43.555	β = 99.37
c = 82.049	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	PIXEL	DECTRIS PILATUS 6M		2013-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96861	Diamond	I24

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	2.6	80.955	94.9	0.116	7.4	2.7	14800	14800	1	1	43

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	2.6	2.72	94.8		0.754	1.8	2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19	2.6	29.74	1.35	14779	14779	691	94.06	0.2409	0.2392	0.24	0.2747	0.28

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	11.531
f_angle_d	0.658
f_chiral_restr	0.043
f_bond_d	0.003
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3212
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	97

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	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.