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Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with glutamate and positive allosteric modulator BPAM538
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 279 18% PEG4000, 0.23M lithium-sulfate, 0.1M phosphate-citrate
Crystal Properties Matthews coefficient Solvent content 2.54 51.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.702 α = 90 b = 164.374 β = 90 c = 47.328 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 CCD MARMOSAIC 225 mm CCD 2013-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.00000 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2 29.27 99.8 0.087 0.099 0.046 10.3 4.1 61361 61361 20.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.313 0.313 0.359 0.172 2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3TDJ 2 28.521 1.35 61325 3110 99.74 0.1684 0.1673 0.1762 0.1889 0.1955 26.8321
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.13 f_angle_d 0.606 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6096 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 136
Software Software Software Name Purpose SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction XDS data reduction