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Crystal structure of the GluR5 ligand binding core dimer in complex with UBP315 at 1.80 Angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F34 pdb entry 2F34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.9 293 18% PEG 1K, 100 mM Tris-Cl, 2.5 mM UBP315, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.823 α = 90 b = 97.816 β = 90 c = 129.043 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2006-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
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 1.8 40 99.9 0.04 20.9 3.5 57347 57347 1 1 27.42
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 1.8 1.86 99.8 0.273 4.73 3.4
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 FOURIER SYNTHESIS THROUGHOUT pdb entry 2F34 1.8 21.57 54463 54463 2884 99.91 0.19864 0.19864 0.19756 0.2058 0.21916 0.2231 RANDOM 34.393
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 r_dihedral_angle_2_deg 30.37 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 5.261 r_scangle_it 1.9 r_angle_refined_deg 1.331 r_scbond_it 1.294 r_mcangle_it 0.867 r_mcbond_it 0.523 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.37 r_dihedral_angle_4_deg 13.754 r_dihedral_angle_3_deg 13.738 r_dihedral_angle_1_deg 5.261 r_scangle_it 1.9 r_angle_refined_deg 1.331 r_scbond_it 1.294 r_mcangle_it 0.867 r_mcbond_it 0.523 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.087 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4014 Nucleic Acid Atoms Solvent Atoms 366 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling