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Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5
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 3.26 62.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 268.43 α = 90 b = 60.633 β = 116.42 c = 145.391 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 2017-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.91979 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.72 29.88 98.6 0.065 0.077 0.041 0.999 14.4 3.5 56030
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 2.72 2.79 93.9 0.958 1.152 0.632 0.598 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 2.72 25 53230 2761 98.14 0.1909 0.1887 0.1914 0.2343 0.2359 RANDOM 73.422
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] -2.47 -1.97 2.88 1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 8.038 r_angle_other_deg 0.398 r_angle_refined_deg 0.379 r_chiral_restr 0.032 r_gen_planes_refined 0.01 r_bond_refined_d 0.001 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.56 r_dihedral_angle_4_deg 19.999 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 8.038 r_angle_other_deg 0.398 r_angle_refined_deg 0.379 r_chiral_restr 0.032 r_gen_planes_refined 0.01 r_bond_refined_d 0.001 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10948 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 268
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing