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Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31
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 61.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 268.62 α = 90 b = 59.595 β = 117.1 c = 145.914 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 2.262 35 98.6 0.068 0.081 0.042 8.8 3.4 92724
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 2.27 2.32 97.3 1.091 1.315 0.723 0.472 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3QEL 2.27 25 74940 3926 82.03 0.2041 0.2024 0.2074 0.2367 0.2373 RANDOM 39.604
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] -0.21 0.56 -0.66 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.99 r_dihedral_angle_4_deg 22.294 r_dihedral_angle_3_deg 15.718 r_dihedral_angle_1_deg 8.451 r_angle_other_deg 0.412 r_angle_refined_deg 0.345 r_chiral_restr 0.034 r_gen_planes_refined 0.02 r_bond_refined_d 0.005 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.99 r_dihedral_angle_4_deg 22.294 r_dihedral_angle_3_deg 15.718 r_dihedral_angle_1_deg 8.451 r_angle_other_deg 0.412 r_angle_refined_deg 0.345 r_chiral_restr 0.034 r_gen_planes_refined 0.02 r_bond_refined_d 0.005 r_gen_planes_other 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10977 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing