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Structure of the ligand-binding core of the ionotropic glutamate receptor-like GluRdelta2 in complex with D-serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V3T PDB ENTRY 2V3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 HANGING DROP VAPOR DIFFUSION. 20% PEG4000, 0.1 M CACODYLATE PH 6.5, 0.2 M SODIUM THIOCYANATE
Crystal Properties Matthews coefficient Solvent content 2 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.801 α = 66.88 b = 40.307 β = 79.31 c = 44.393 γ = 86.46
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 2006-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.73 40 92.3 0.04 12 3.8 23508 6 23.59
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 1.73 1.82 70.1 0.26 2.1 3.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2V3T 1.74 40.19 21250 1154 95.3 0.2 0.197 0.25 RANDOM 24.16
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] -0.73 0.26 0.54 0.64 -0.07 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.776 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 11.478 r_scangle_it 3.785 r_scbond_it 2.415 r_mcangle_it 1.75 r_angle_refined_deg 1.526 r_mcbond_it 1.019 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.776 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 15.315 r_dihedral_angle_1_deg 11.478 r_scangle_it 3.785 r_scbond_it 2.415 r_mcangle_it 1.75 r_angle_refined_deg 1.526 r_mcbond_it 1.019 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.111 r_bond_refined_d 0.016 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined 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 2022 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing