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Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-cysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R85
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 100 mM HEPES pH 7.5, sodium citrate tribasic 1.4 M
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.661 α = 90 b = 98.544 β = 90 c = 114.154 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 EIGER X 16M 2018-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 2.5 49.4 100 0.272 0.295 0.113 0.986 6 6.7 38874
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 2.5 2.6 100 1.613 1.745 0.662 0.578 6.9
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 6R85 2.5 49.4 36927 2108 99.97 0.1901 0.1882 0.1888 0.2276 0.2266 RANDOM 35.47
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] 2.75 -0.92 -1.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.369 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 16.279 r_dihedral_angle_1_deg 7.273 r_angle_refined_deg 1.473 r_angle_other_deg 1.262 r_chiral_restr 0.155 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.369 r_dihedral_angle_4_deg 18.681 r_dihedral_angle_3_deg 16.279 r_dihedral_angle_1_deg 7.273 r_angle_refined_deg 1.473 r_angle_other_deg 1.262 r_chiral_restr 0.155 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7400 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction