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Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Crystal Properties Matthews coefficient Solvent content 3.21 61.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 267.953 α = 90 b = 59.898 β = 116.69 c = 145.286 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 16M 2016-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 35 98.8 0.048 0.055 0.027 10.4 4 119094
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 96.8 1.039 1.224 0.632 0.585 3.2
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 3QEL 2.1 25 95244 5143 83.23 0.1902 0.1887 0.1966 0.2184 0.2228 RANDOM 38.17
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] -0.39 0.34 -0.38 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.757 r_dihedral_angle_4_deg 25.206 r_dihedral_angle_3_deg 15.938 r_dihedral_angle_1_deg 8.277 r_angle_other_deg 0.418 r_angle_refined_deg 0.375 r_chiral_restr 0.04 r_gen_planes_refined 0.012 r_bond_refined_d 0.006 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.757 r_dihedral_angle_4_deg 25.206 r_dihedral_angle_3_deg 15.938 r_dihedral_angle_1_deg 8.277 r_angle_other_deg 0.418 r_angle_refined_deg 0.375 r_chiral_restr 0.04 r_gen_planes_refined 0.012 r_bond_refined_d 0.006 r_gen_planes_other 0.001 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10945 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing