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Structure of glutamate receptor-like channel GLR3.4 ligand-binding domain in complex with glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VEA PDB entry 6VEA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 277 2 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.337 α = 90 b = 74.337 β = 90 c = 513.56 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS 6M-F 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 2.29 64.46 99.7 0.123 0.13 0.042 0.998 12.9 9.3 39519
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 2.29 2.37 97 0.809 0.856 0.275 0.805 9.2
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 PDB entry 6VEA 2.29 64.46 37406 1962 99.62 0.2112 0.2095 0.2168 0.2426 0.2456 RANDOM 36.822
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] -0.61 -0.31 -0.61 1.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.378 r_dihedral_angle_3_deg 14.413 r_dihedral_angle_4_deg 12.657 r_dihedral_angle_1_deg 6.687 r_angle_refined_deg 1.251 r_angle_other_deg 1.145 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.378 r_dihedral_angle_3_deg 14.413 r_dihedral_angle_4_deg 12.657 r_dihedral_angle_1_deg 6.687 r_angle_refined_deg 1.251 r_angle_other_deg 1.145 r_chiral_restr 0.052 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5877 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 53
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction