2ZNU

Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, GluR5, in complex with a novel selective agonist, neodysiherbaine A

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	279	PEG3350, NaCl, EDTA, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.886	α = 90
b = 64.99	β = 107.29
c = 50.232	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	100	CCD	ADSC QUANTUM 270		2007-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

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	1.8	50	99.3	0.056	27.6	3.7		33702

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)
	1.8	1.86	96.3		0.294	1.87	2.9	3245

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 2ZNS	1.8	30	32025	1674	99.24	0.19367	0.19142	0.23708	RANDOM	30.816

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]
0.31		-0.4	1.12		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.91
r_dihedral_angle_4_deg	13.865
r_dihedral_angle_3_deg	13.43
r_dihedral_angle_1_deg	5.906
r_scangle_it	3.131
r_scbond_it	2.034
r_mcangle_it	1.406
r_angle_refined_deg	1.372
r_mcbond_it	0.921
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.91
r_dihedral_angle_4_deg	13.865
r_dihedral_angle_3_deg	13.43
r_dihedral_angle_1_deg	5.906
r_scangle_it	3.131
r_scbond_it	2.034
r_mcangle_it	1.406
r_angle_refined_deg	1.372
r_mcbond_it	0.921
r_nbtor_refined	0.305
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.183
r_xyhbond_nbd_refined	0.147
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.104
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2067
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
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 R01GM133198.