2ZNT | pdb_00002znt

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

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 = 118.851	α = 90
b = 65.137	β = 107.03
c = 50.059	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	1.6	50	96.2	0.044	36.9	3.7		46169

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)
	1.6	1.66	76.9		0.239	2.27	3.1	3692

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 (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 2ZNS	1.6	30	43859	2307	96.01	0.20029	0.19895	0.19	0.22538	0.22	RANDOM	27.956

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]
0.25		-0.64	0.96		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.382
r_dihedral_angle_4_deg	15.563
r_dihedral_angle_3_deg	13.301
r_dihedral_angle_1_deg	11.133
r_scangle_it	2.668
r_scbond_it	1.77
r_angle_refined_deg	1.337
r_mcangle_it	1.215
r_mcbond_it	0.81
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.382
r_dihedral_angle_4_deg	15.563
r_dihedral_angle_3_deg	13.301
r_dihedral_angle_1_deg	11.133
r_scangle_it	2.668
r_scbond_it	1.77
r_angle_refined_deg	1.337
r_mcangle_it	1.215
r_mcbond_it	0.81
r_nbtor_refined	0.306
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.186
r_symmetry_hbond_refined	0.116
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2131
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	41

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 R01GM157729.