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Crystal structure of GluR5 ligand-binding core in complex with lithium at 1.49 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TT1 PDB entry 1TT1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20% PEG 4000, 125 mM LiCl, 175 mM Li2(SO4), 100 mM Li cacodylate, 4 mM Kainic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.529 α = 90 b = 70.529 β = 90 c = 234.128 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 300 mm CCD 2007-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.49 35 97.6 0.055 13.5 7.3 97909 97909 16.17
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 1.49 1.54 92.2 0.415 3.9 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1TT1 1.49 34.88 90487 90487 4817 97.73 0.16655 0.16655 0.16527 0.1636 0.19024 0.1884 RANDOM 14.038
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 13.292 r_dihedral_angle_1_deg 5.848 r_scangle_it 4.156 r_scbond_it 2.754 r_angle_refined_deg 1.731 r_mcangle_it 1.7 r_mcbond_it 1.155 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.649 r_dihedral_angle_4_deg 18.641 r_dihedral_angle_3_deg 13.292 r_dihedral_angle_1_deg 5.848 r_scangle_it 4.156 r_scbond_it 2.754 r_angle_refined_deg 1.731 r_mcangle_it 1.7 r_mcbond_it 1.155 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.214 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.165 r_metal_ion_refined 0.145 r_chiral_restr 0.127 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4048 Nucleic Acid Atoms Solvent Atoms 690 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing