3H6W

Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5217 at 1.50 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FTJPDB entry 1FTJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527920 % PEG 4000, 0.1 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties
Matthews coefficientSolvent content
2.2545.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.01α = 90
b = 47.179β = 91.88
c = 118.412γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8080EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.4917.3885.60.0410.04125.23.77232518
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.491.5595.40.4050.4052.68047

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1FTJ1.4917.3871603139284.510.1890.232RANDOM19.9
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]
0.760.84-1.330.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.659
r_dihedral_angle_4_deg21.63
r_dihedral_angle_3_deg13.571
r_dihedral_angle_1_deg5.768
r_sphericity_free4.937
r_scangle_it2.987
r_scbond_it2.235
r_sphericity_bonded2.065
r_mcangle_it1.44
r_angle_refined_deg1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.659
r_dihedral_angle_4_deg21.63
r_dihedral_angle_3_deg13.571
r_dihedral_angle_1_deg5.768
r_sphericity_free4.937
r_scangle_it2.987
r_scbond_it2.235
r_sphericity_bonded2.065
r_mcangle_it1.44
r_angle_refined_deg1.36
r_mcbond_it1.202
r_rigid_bond_restr1.153
r_angle_other_deg0.872
r_mcbond_other0.39
r_nbd_refined0.213
r_nbd_other0.19
r_nbtor_refined0.182
r_symmetry_vdw_other0.182
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.131
r_symmetry_vdw_refined0.125
r_nbtor_other0.09
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4081
Nucleic Acid Atoms
Solvent Atoms683
Heterogen Atoms96

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection