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Structure of the Glutamate-Like Receptor GLR3.2 ligand-binding domain in complex with Glycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 22 % PEG 4000,
0.1 M Ammonium acetate,
0.1 M Sodium acetate pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.15 42.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.389 α = 90 b = 64.37 β = 90 c = 75.933 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 2019-11-06 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 1.58 47.39 99.2 0.062 0.069 0.031 0.999 14.9 4.6 32133
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 1.58 1.61 98.7 0.612 0.713 0.356 0.696 2.1 3.7
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 6VE8 1.58 40.23 30524 1573 98.67 0.1588 0.1575 0.1693 0.1837 0.1958 RANDOM 19.238
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] -0.6 -0.63 1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.466 r_dihedral_angle_4_deg 17.071 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 6.751 r_angle_refined_deg 1.857 r_angle_other_deg 1.547 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.466 r_dihedral_angle_4_deg 17.071 r_dihedral_angle_3_deg 13.321 r_dihedral_angle_1_deg 6.751 r_angle_refined_deg 1.857 r_angle_other_deg 1.547 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1847 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction