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Crystal Structure of the GluR5 Ligand Binding Core Dimer with UBP310 At 1.74 Angstroms Resolution
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 8.6 293 17-22% PEG 1K
100mM TRIS
5mM UBP310, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.64 53.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.698 α = 90 b = 97.954 β = 90 c = 129.126 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 MARRESEARCH 2005-08-11 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 1.74 40 99.9 0.038 14.5 4.9 64151 64151 1 1 25.16
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 1.74 1.8 99.7 0.441 3.38 4.9
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 1TXF 1.74 33.41 60378 60378 3218 99.92 0.18255 0.18255 0.18103 0.1833 0.21135 0.1872 RANDOM 19.284
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] 0.26 0.21 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.879 r_dihedral_angle_4_deg 13.203 r_dihedral_angle_3_deg 10.626 r_dihedral_angle_1_deg 2.762 r_scangle_it 1.876 r_mcangle_it 1.718 r_angle_refined_deg 1.661 r_scbond_it 1.33 r_mcbond_it 1.123 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.879 r_dihedral_angle_4_deg 13.203 r_dihedral_angle_3_deg 10.626 r_dihedral_angle_1_deg 2.762 r_scangle_it 1.876 r_mcangle_it 1.718 r_angle_refined_deg 1.661 r_scbond_it 1.33 r_mcbond_it 1.123 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.262 r_xyhbond_nbd_refined 0.228 r_symmetry_hbond_refined 0.227 r_chiral_restr 0.124 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_refined 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 4014 Nucleic Acid Atoms Solvent Atoms 482 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing