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Differences between the GluD1 and GluD2 receptors revealed by GluD1 X-ray crystallography, binding studies and molecular dynamics
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 24.4% PEG 4000, 0.1M ammonium sulfate, 0.1 cacodylate
Crystal Properties Matthews coefficient Solvent content 2.13 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.31 α = 90 b = 136.44 β = 96.98 c = 54.61 γ = 90
Symmetry Space Group P 1 21 1
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 2018-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.79 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.57 68.22 99.8 0.127 0.146 0.993 8.73 3.936 15301 35.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.57 2.64 100 0.61 0.705 0.727 2.11 3.95
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 THROUGHOUT 2V3T 2.574 68.22 1.35 15291 759 99.71 0.2166 0.2148 0.2181 0.2515 0.2502 38.5737
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 12.977 f_angle_d 0.575 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4068 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction AutoProcess data processing XSCALE data scaling PHASER phasing TRUNCATE data reduction