4MR9 | pdb_00004mr9

Crystal structure of the extracellular domain of human GABA(B) receptor bound to the antagonist SCH50911

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MQE	PDB ENTRY 4MQE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	10% PEG3350, 20% glycerol, 0.12 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.5	α = 90
b = 113.07	β = 96.96
c = 73.22	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315		2011-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97949	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.35	113.07	99.6	0.041	0.041	18.2	3.8	46629	46629			65.21

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.48	99.9		0.678	0.678	1.1	3.8	6803

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4MQE	2.35	72.68	46593	46593	2347	99.53	0.208	0.208	0.2069	0.22	0.2288	0.24	RANDOM	69.3759

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]
-0.9496		6.4574	-10.97		11.9196

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	17.39
t_torsion_other	17.39
t_omega_torsion	2.85
t_it	1.289
t_angle_deg	1.15
t_gen_planes	0.015
t_bond_d	0.01
t_trig_c_planes	0.0068

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6485
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	99

Software

Software
Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	phasing
BUSTER	refinement

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.