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Exploring the GluR2 ligand-binding core in complex with the bicyclic AMPA analogue (S)-4-AHCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 279 PEG 3350, phosphate-citrate buffer, lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.3 46.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.412 α = 90 b = 59.467 β = 90 c = 47.845 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 110 CCD MARRESEARCH 2003-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.811 EMBL/DESY, HAMBURG X11
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 1.75 20.08 99.1 0.037 26.7 3.5 27472 27472 -3 -3 18.1
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 1.75 1.78 96.3 0.227 4.1 1333
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1M5C 1.75 20.08 27450 26073 1376 99.08 0.17111 0.17111 0.16882 0.1726 0.21418 RANDOM 20.624
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] 0.27 -1.01 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.746 r_scangle_it 4.75 r_scbond_it 2.924 r_mcangle_it 1.706 r_angle_refined_deg 1.599 r_mcbond_it 0.993 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.746 r_scangle_it 4.75 r_scbond_it 2.924 r_mcangle_it 1.706 r_angle_refined_deg 1.599 r_mcbond_it 0.993 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.113 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2039 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing