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Crystal structure of the GluA2o LBD in complex with glutamate and LY451395
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.9 277 15% PEG 3350, 0.1 M sodium acetate, and 0.1 M zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.48 50.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.724 α = 90 b = 161.913 β = 89.97 c = 46.964 γ = 90
Symmetry Space Group P 1 21 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 210r 2007-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1 ALS 5.0.3
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 1.52 50 99.6 0.057 20.4 4 258897
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) 1 1.52 1.56 96.4 0.546 1.9 3
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 1FTJ 1.52 40 245610 13000 99.4 0.20397 0.20239 0.2037 0.23342 0.2066 RANDOM 27.957
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] 0.05 0.07 0.12 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.486 r_dihedral_angle_4_deg 15.502 r_dihedral_angle_3_deg 13.242 r_long_range_B_refined 5.902 r_dihedral_angle_1_deg 5.735 r_scbond_it 2.441 r_mcangle_it 2.328 r_mcbond_it 1.626 r_angle_refined_deg 1.447 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.486 r_dihedral_angle_4_deg 15.502 r_dihedral_angle_3_deg 13.242 r_long_range_B_refined 5.902 r_dihedral_angle_1_deg 5.735 r_scbond_it 2.441 r_mcangle_it 2.328 r_mcbond_it 1.626 r_angle_refined_deg 1.447 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12224 Nucleic Acid Atoms Solvent Atoms 1242 Heterogen Atoms 189
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing