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Structure of the Glutamate-Like Receptor GLR3.2 ligand-binding domain in complex with Methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MMS Homology model based on 6MMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M MES pH 6.5,
18% PEG MME 2K,
0.1 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.645 α = 90 b = 65.47 β = 90 c = 72.186 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97910 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.75 72.19 99.8 0.078 0.087 0.037 0.998 13.3 5.3 23419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 99.1 0.674 0.806 0.433 0.655 1.8 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Homology model based on 6MMS 1.75 48.5 22200 1167 99.74 0.1667 0.165 0.1783 0.1997 0.2065 RANDOM 22.065
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] -0.76 -0.71 1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.15 r_dihedral_angle_4_deg 16.076 r_dihedral_angle_3_deg 13.419 r_dihedral_angle_1_deg 6.84 r_angle_refined_deg 1.721 r_angle_other_deg 1.445 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.15 r_dihedral_angle_4_deg 16.076 r_dihedral_angle_3_deg 13.419 r_dihedral_angle_1_deg 6.84 r_angle_refined_deg 1.721 r_angle_other_deg 1.445 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1830 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing