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CNQX bound to an oxidized double cysteine mutant (A452C/S652C) of the ligand binding domain of GluA2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DP6 PDB ENTRY 3DP6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 14-15% PEG8000, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.724 α = 90 b = 165.243 β = 90 c = 47.651 γ = 90
Symmetry Space Group P 21 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 ADSC QUANTUM 210 2010-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.977 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.97 50 92.8 0.05 0.05 47.657 6.4 60254 60254 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2 98 0.165 0.165 9.84 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3DP6 1.97 33.5 56778 3039 92.07 0.168 0.16531 0.21883 0.2399 RANDOM 22.76
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.654 r_dihedral_angle_4_deg 16.975 r_dihedral_angle_3_deg 15.202 r_dihedral_angle_1_deg 6.07 r_scangle_it 5.381 r_scbond_it 3.366 r_mcangle_it 2.047 r_angle_refined_deg 1.867 r_mcbond_it 1.187 r_angle_other_deg 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.654 r_dihedral_angle_4_deg 16.975 r_dihedral_angle_3_deg 15.202 r_dihedral_angle_1_deg 6.07 r_scangle_it 5.381 r_scbond_it 3.366 r_mcangle_it 2.047 r_angle_refined_deg 1.867 r_mcbond_it 1.187 r_angle_other_deg 1.12 r_mcbond_other 0.377 r_chiral_restr 0.161 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6044 Nucleic Acid Atoms Solvent Atoms 908 Heterogen Atoms 56
Software Software Software Name Purpose HKL-3000 data collection PHENIX model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing