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Crystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-521 at 2.18 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E0X PDB entry 4E0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 279 16 % PEG4000, 0.2 M lithium-sulfate, 0.1 M phosphate-citrate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.777 α = 90 b = 68.777 β = 90 c = 232.891 γ = 90
Symmetry Space Group P 41 21 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 CCD MARMOSAIC 225 mm CCD 2014-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.97879 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.181 47.606 97.8 0.074 14.4 5.8 29453 27.92
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 2.181 2.3 87.6 0.152 4.6 2.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4E0X 2.181 47.606 1.36 29430 1497 97.43 0.1689 0.1665 0.168 0.2148 0.2157 Random selection 29.89
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 13.561 f_angle_d 1.045 f_chiral_restr 0.067 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3996 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling XSCALE data reduction