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Crystal structure of the ligand-binding core of the human ionotropic glutamate receptor, GluR5, in complex with glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TXF PDB ENTRY 1TXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 279 PEG3350, NaCl, EDTA, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 3.13 60.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.391 α = 90 b = 63.576 β = 106.73 c = 50.147 γ = 90
Symmetry Space Group C 1 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 CCD ADSC QUANTUM 210 2007-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 SPring-8 BL44B2
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 30 99.7 0.089 18.9 3.7 24561 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 98.7 0.315 1.62 3.5 2407
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 PDB ENTRY 1TXF 2 30 23097 1242 99.74 0.19547 0.19381 0.1901 0.22548 0.2246 RANDOM 46.573
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] 2.21 -1.36 -0.84 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.147 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 16.619 r_dihedral_angle_1_deg 6.918 r_scangle_it 3.913 r_scbond_it 2.755 r_angle_refined_deg 1.751 r_mcangle_it 1.747 r_mcbond_it 1.147 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.147 r_dihedral_angle_4_deg 17.51 r_dihedral_angle_3_deg 16.619 r_dihedral_angle_1_deg 6.918 r_scangle_it 3.913 r_scbond_it 2.755 r_angle_refined_deg 1.751 r_mcangle_it 1.747 r_mcbond_it 1.147 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.149 r_symmetry_hbond_refined 0.113 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2041 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing