2ZNS

Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, GluR5, in complex with glutamate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TXF	PDB ENTRY 1TXF

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
3.13	60.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.391	α = 90
b = 63.576	β = 106.73
c = 50.147	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 210		2007-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44B2	1.0	SPring-8	BL44B2

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	2	30	99.7	0.089	18.9	3.7		24561	2	2

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)
	2	2.07	98.7		0.315	1.62	3.5	2407

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 1TXF	2	30	23097	1242	99.74	0.19547	0.19381	0.22548	RANDOM	46.573

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]
2.21		-1.36	-0.84		-2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.147
r_dihedral_angle_4_deg	17.51
r_dihedral_angle_3_deg	16.619
r_dihedral_angle_1_deg	6.918
r_scangle_it	3.913
r_scbond_it	2.755
r_angle_refined_deg	1.751
r_mcangle_it	1.747
r_mcbond_it	1.147
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.147
r_dihedral_angle_4_deg	17.51
r_dihedral_angle_3_deg	16.619
r_dihedral_angle_1_deg	6.918
r_scangle_it	3.913
r_scbond_it	2.755
r_angle_refined_deg	1.751
r_mcangle_it	1.747
r_mcbond_it	1.147
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.149
r_symmetry_hbond_refined	0.113
r_bond_refined_d	0.019
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2041
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	10

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.