☰ Navigation Tabs
Crystal structure of the GluR5 ligand binding core dimer in complex with UBP316 at 1.76 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 8.8 293 18% PEG 1K, 100mM Tris-Cl, 2.5mM UBP316, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.766 α = 90 b = 97.702 β = 90 c = 128.604 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 CCD MARMOSAIC 300 mm CCD 2006-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 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 1.76 40 98.2 0.037 13.8 5.3 61223 61223 1 1 24.47
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 1.76 1.82 98.6 0.381 4 5.3
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 1.76 32.22 57079 57079 3022 98.27 0.18897 0.18897 0.18746 0.1869 0.21814 0.2181 RANDOM 30.78
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 33.055 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_4_deg 13.307 r_dihedral_angle_1_deg 5.013 r_scangle_it 1.896 r_scbond_it 1.219 r_angle_refined_deg 1.185 r_mcangle_it 0.872 r_mcbond_it 0.515 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.055 r_dihedral_angle_3_deg 13.698 r_dihedral_angle_4_deg 13.307 r_dihedral_angle_1_deg 5.013 r_scangle_it 1.896 r_scbond_it 1.219 r_angle_refined_deg 1.185 r_mcangle_it 0.872 r_mcbond_it 0.515 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.183 r_xyhbond_nbd_refined 0.143 r_symmetry_hbond_refined 0.105 r_chiral_restr 0.076 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 409 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement SERGUI data collection HKL-2000 data reduction HKL-2000 data scaling