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NMDA bound to compound 380
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 282.15 10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.972 α = 90 b = 90.036 β = 90 c = 123.174 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M-F 2018-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.948 72.7 100 0.143 0.061 0.996 8.2 6.4 44610
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 0.823 0.37 0.613 2.2 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.948 72.7 44423 2309 99.46 0.206 0.2032 0.2564 0.2481 RANDOM 29.563
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] -0.639 -0.37 1.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.222 r_dihedral_angle_6_deg 14.069 r_dihedral_angle_3_deg 13.742 r_lrange_it 7.692 r_lrange_other 7.692 r_dihedral_angle_1_deg 6.797 r_scangle_it 4.874 r_scangle_other 4.873 r_mcangle_it 4.151 r_mcangle_other 4.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.222 r_dihedral_angle_6_deg 14.069 r_dihedral_angle_3_deg 13.742 r_lrange_it 7.692 r_lrange_other 7.692 r_dihedral_angle_1_deg 6.797 r_scangle_it 4.874 r_scangle_other 4.873 r_mcangle_it 4.151 r_mcangle_other 4.15 r_scbond_other 3.175 r_scbond_it 3.173 r_mcbond_it 2.627 r_mcbond_other 2.627 r_angle_refined_deg 1.494 r_angle_other_deg 0.507 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.176 r_nbd_other 0.175 r_symmetry_nbd_other 0.172 r_chiral_restr_other 0.163 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.107 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4302 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing