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Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an allosteric modulator
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O28
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 277 18% PEG 4000, 50mM Lithium Sulphate, 2.5% Glycerol, 100mM Sodium Cacodylate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.22 α = 90 b = 87.23 β = 90 c = 47.4 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ Mirrors 2007-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.79 43.61 98.1 0.05 13.2 4.1 24891 24891 2 26.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 82.9 0.287 3.5 2.9 2050
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3O28 1.8 43.61 23631 23631 1259 98.1 0.1987 0.18716 0.18394 0.1853 0.25232 0.2597 RANDOM 18.709
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] -0.33 1.04 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.004 r_dihedral_angle_4_deg 18.652 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_1_deg 5.919 r_scangle_it 4.305 r_scbond_it 3.213 r_mcangle_it 1.953 r_mcbond_it 1.724 r_angle_refined_deg 1.613 r_angle_other_deg 1.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.004 r_dihedral_angle_4_deg 18.652 r_dihedral_angle_3_deg 14.404 r_dihedral_angle_1_deg 5.919 r_scangle_it 4.305 r_scbond_it 3.213 r_mcangle_it 1.953 r_mcbond_it 1.724 r_angle_refined_deg 1.613 r_angle_other_deg 1.357 r_mcbond_other 0.395 r_symmetry_hbond_refined 0.273 r_symmetry_vdw_refined 0.251 r_symmetry_vdw_other 0.232 r_nbd_refined 0.205 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.174 r_chiral_restr 0.097 r_nbtor_other 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2043 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 86
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement d*TREK data reduction d*TREK data scaling