2F36

Crystal Structure of the GluR5 Ligand Binding Core Dimer with Glutamate At 2.1 Angstroms Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TXFPDB 1TXf

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12931.75 M Ammonium Sulfate 100 mM HEPES 10 mM glutamic acid, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.694α = 90
b = 73.784β = 99.74
c = 115.918γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID0.99997APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.13099.80.08412.33.453310533102.111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.181000.3443.62

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB 1TXf2.1129.87533105331060161000.191240.191240.185620.24111RANDOM28.726
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]
-0.130.370.140.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.596
r_dihedral_angle_4_deg13.914
r_dihedral_angle_3_deg11.392
r_dihedral_angle_1_deg2.689
r_mcangle_it2.323
r_scangle_it2.208
r_angle_refined_deg1.839
r_mcbond_it1.529
r_scbond_it1.51
r_symmetry_hbond_refined0.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.596
r_dihedral_angle_4_deg13.914
r_dihedral_angle_3_deg11.392
r_dihedral_angle_1_deg2.689
r_mcangle_it2.323
r_scangle_it2.208
r_angle_refined_deg1.839
r_mcbond_it1.529
r_scbond_it1.51
r_symmetry_hbond_refined0.326
r_nbtor_refined0.322
r_symmetry_vdw_refined0.291
r_nbd_refined0.238
r_xyhbond_nbd_refined0.227
r_chiral_restr0.144
r_bond_refined_d0.016
r_gen_planes_refined0.007
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 Atoms8008
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing