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Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QEL PDB entry 3QEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 sodium formate, HEPES, sodium chloride, Tris
Crystal Properties Matthews coefficient Solvent content 3.23 61.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 269.172 α = 90 b = 60.076 β = 117.02 c = 145.572 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER X 9M 2018-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9198 NSLS-II 17-ID-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 2.85 50 99.1 0.073 14.7 3.3 48988
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 2.85 2.9 0.776
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 3QEL 2.85 34.37 39153 2034 84.01 0.17782 0.1743 0.24579 0.255 RANDOM 51.906
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] 0.64 -1.69 2.54 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.65 r_long_range_B_refined 11.378 r_long_range_B_other 11.377 r_dihedral_angle_1_deg 8.139 r_mcangle_it 7.992 r_mcangle_other 7.992 r_scangle_other 7.914 r_dihedral_angle_2_deg 7.867 r_mcbond_it 5.079 r_mcbond_other 5.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.65 r_long_range_B_refined 11.378 r_long_range_B_other 11.377 r_dihedral_angle_1_deg 8.139 r_mcangle_it 7.992 r_mcangle_other 7.992 r_scangle_other 7.914 r_dihedral_angle_2_deg 7.867 r_mcbond_it 5.079 r_mcbond_other 5.079 r_scbond_it 5.062 r_scbond_other 5.062 r_angle_refined_deg 1.527 r_angle_other_deg 0.51 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11085 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 221
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing