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Crystal structure of the amino-terminal domain (ATD) of iGluR Delta-1 (GluD1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES (2-ethanesulfonic acid)/imidazole pH 6.5, 10% (w/v) polyethylene glycol 8000, 20% (w/v) ethylene glycol, 0.02 M 1,6-hexanediol, 0.02 M (RS)-1,2-propanediol, 0.02 M 1-butanol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol and 0.02 M 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.42 α = 90 b = 128.42 β = 90 c = 153.23 γ = 120
Symmetry Space Group P 32 2 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 PILATUS 2M 2012-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.3 59.22 99.7 0.051 1 22.6 8.5 65080 57.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 98.5 1.222 1.9 8.7
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 FREE R-VALUE 5KC8 2.3 59.22 1.34 65074 3276 99.68 0.2006 0.1992 0.2113 0.2273 0.2386 77.6
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 12.186 f_angle_d 0.855 f_chiral_restr 0.036 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9096 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 197
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing