3FVK

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

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FVNPDB ENTRY 3FVN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.530335% PEG3350, 0.3M LiSO4, 5mM 8-deoxy-neodysiherbaine, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
2.2645.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.508α = 80.43
b = 50.787β = 84.41
c = 62.644γ = 62.1
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95IMAGE PLATEMAR scanner 345 mm plate2008-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B20.9SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.550960.03635.93.878332
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5587.40.2613.23.27117

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3FVN1.53074370391895.860.167270.165940.19148RANDOM18.303
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]
-0.220.15-0.01-0.540.140.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.101
r_dihedral_angle_3_deg13.129
r_dihedral_angle_4_deg12.829
r_dihedral_angle_1_deg5.476
r_scangle_it2.777
r_scbond_it1.85
r_angle_refined_deg1.242
r_mcangle_it1.188
r_mcbond_it0.781
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.101
r_dihedral_angle_3_deg13.129
r_dihedral_angle_4_deg12.829
r_dihedral_angle_1_deg5.476
r_scangle_it2.777
r_scbond_it1.85
r_angle_refined_deg1.242
r_mcangle_it1.188
r_mcbond_it0.781
r_nbtor_refined0.308
r_nbd_refined0.196
r_symmetry_vdw_refined0.181
r_symmetry_hbond_refined0.124
r_xyhbond_nbd_refined0.11
r_chiral_restr0.088
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms4035
Nucleic Acid Atoms
Solvent Atoms371
Heterogen Atoms101

Software

Software
Software NamePurpose
MAR345dtbdata collection
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing