3KGC

Isolated ligand binding domain dimer of GluA2 ionotropic glutamate receptor in complex with glutamate, LY 404187 and ZK 200775


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FTLPDB entry 1FTL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP527719% PEG 4000, 0.3 M ammonium sulfate, 0.1 M sodium acetate, pH 5.0, vapor diffusion, hanging drop, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6453.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.657α = 90
b = 95.586β = 90
c = 97.047γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 3152007-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.555081451

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 1FTL1.5536.06381451430794.780.19770.196280.22447RANDOM15.409
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]
-0.130.44-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.518
r_dihedral_angle_4_deg19.512
r_dihedral_angle_3_deg11.998
r_dihedral_angle_1_deg6.983
r_scangle_it2.914
r_scbond_it1.944
r_angle_refined_deg1.321
r_mcangle_it1.171
r_mcbond_it0.736
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.518
r_dihedral_angle_4_deg19.512
r_dihedral_angle_3_deg11.998
r_dihedral_angle_1_deg6.983
r_scangle_it2.914
r_scbond_it1.944
r_angle_refined_deg1.321
r_mcangle_it1.171
r_mcbond_it0.736
r_nbtor_refined0.306
r_nbd_refined0.205
r_xyhbond_nbd_refined0.114
r_symmetry_hbond_refined0.113
r_symmetry_vdw_refined0.11
r_chiral_restr0.094
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms3867
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement