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Crystal structure of the GluA2 LBD (L483Y-N754S-L758V) in complex with glutamate
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 7 277.15 20% w/v PEG3350, 200mM Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.23 44.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.99 α = 90 b = 121.297 β = 90 c = 47.083 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 PIXEL PSI PILATUS 6M mirror 2014-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.44 48 99.2 11.65 4.27 99346
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 FREE R-VALUE 1FTJ 1.44 47.99 94378 4968 99.19 0.1501 0.14722 0.1473 0.20486 0.205 RANDOM 19.624
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] 0.03 0.72 -0.75
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.226 r_dihedral_angle_2_deg 30.783 r_dihedral_angle_4_deg 15.445 r_sphericity_bonded 13.808 r_dihedral_angle_3_deg 11.812 r_dihedral_angle_1_deg 6.045 r_long_range_B_refined 4.891 r_rigid_bond_restr 4.05 r_long_range_B_other 3.834 r_scangle_other 3.463
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.226 r_dihedral_angle_2_deg 30.783 r_dihedral_angle_4_deg 15.445 r_sphericity_bonded 13.808 r_dihedral_angle_3_deg 11.812 r_dihedral_angle_1_deg 6.045 r_long_range_B_refined 4.891 r_rigid_bond_restr 4.05 r_long_range_B_other 3.834 r_scangle_other 3.463 r_scbond_it 3.457 r_scbond_other 3.288 r_mcangle_it 2.508 r_mcangle_other 2.508 r_mcbond_it 2.168 r_mcbond_other 2.168 r_angle_refined_deg 2.062 r_angle_other_deg 1.109 r_chiral_restr 0.165 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4083 Nucleic Acid Atoms Solvent Atoms 905 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing