3FV1

Crystal Structure of the human glutamate receptor, GluR5, ligand-binding core in complex with dysiherbaine in space group P1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZNT	PDB ENTRY 2ZNT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	303	35% PEG3350, 0.3M LiSO4, 5mM dysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.486	α = 80.08
b = 50.74	β = 84.18
c = 63.252	γ = 62.06

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	RIGAKU JUPITER 210		2008-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B1	0.9	SPring-8	BL26B1

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	1.5	50	97	0.049	29.6	3.8		79411

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)
	1.5	1.55	95.1		0.193	3.8	3.7	7741

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2ZNT	1.5	30	75397	4011	96.82	0.17154	0.1706	0.18895	RANDOM	12.771

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]
-0.11	0.16	-0.02	-0.25	-0.04	0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.695
r_dihedral_angle_3_deg	12.71
r_dihedral_angle_4_deg	9.997
r_dihedral_angle_1_deg	5.563
r_scangle_it	2.682
r_scbond_it	1.767
r_angle_refined_deg	1.27
r_mcangle_it	1.08
r_mcbond_it	0.924
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.695
r_dihedral_angle_3_deg	12.71
r_dihedral_angle_4_deg	9.997
r_dihedral_angle_1_deg	5.563
r_scangle_it	2.682
r_scbond_it	1.767
r_angle_refined_deg	1.27
r_mcangle_it	1.08
r_mcbond_it	0.924
r_nbtor_refined	0.309
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.161
r_symmetry_hbond_refined	0.124
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4154
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms	85

Software

Software
Software Name	Purpose
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	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.