3FVK | pdb_00003fvk

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-deoxy-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	3FVN	PDB ENTRY 3FVN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	303	35% PEG3350, 0.3M LiSO4, 5mM 8-deoxy-neodysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.508	α = 80.43
b = 50.787	β = 84.41
c = 62.644	γ = 62.1

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	IMAGE PLATE	MAR scanner 345 mm plate		2008-11-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	0.9	SPring-8	BL26B2

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	0.036	35.9	3.8		78332

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	1.5	1.55	87.4		0.261	3.2	3.2	7117

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 3FVN	1.5	30	74370	3918	95.86	0.16727	0.16594	0.16	0.19148	0.19	RANDOM	18.303

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]
-0.22	0.15	-0.01	-0.54	0.14	0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.101
r_dihedral_angle_3_deg	13.129
r_dihedral_angle_4_deg	12.829
r_dihedral_angle_1_deg	5.476
r_scangle_it	2.777
r_scbond_it	1.85
r_angle_refined_deg	1.242
r_mcangle_it	1.188
r_mcbond_it	0.781
r_nbtor_refined	0.308
r_nbd_refined	0.196
r_symmetry_vdw_refined	0.181
r_symmetry_hbond_refined	0.124
r_xyhbond_nbd_refined	0.11
r_chiral_restr	0.088
r_bond_refined_d	0.009
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	4035
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	101

Software

Software
Software Name	Purpose
MAR345dtb	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing