3FV2 | pdb_00003fv2

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with neodysiherbaine A in space group P1

X-RAY DIFFRACTION

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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 neodysiherbaine A, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.579	α = 85.72
b = 50.712	β = 95.79
c = 63.144	γ = 62.08

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	96.9	0.042	32.2	3.8	79267	79267

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		0.157	6.2	3.8	7731

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 2ZNT	1.5	30	75263	3999	96.73	0.1714	0.17016	0.17	0.19456	0.19	RANDOM	9.024

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]
-0.23	0.22	-0.04	-0.32	-0.01	0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.4
r_dihedral_angle_3_deg	12.649
r_dihedral_angle_4_deg	11.196
r_dihedral_angle_1_deg	5.692
r_scangle_it	2.558
r_scbond_it	1.74
r_angle_refined_deg	1.251
r_mcangle_it	1.052
r_mcbond_it	0.737
r_nbtor_refined	0.307
r_nbd_refined	0.193
r_symmetry_vdw_refined	0.172
r_symmetry_hbond_refined	0.119
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.087
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4133
Nucleic Acid Atoms
Solvent Atoms	471
Heterogen Atoms	115

Software

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