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NMDA bound to compound 339
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 2.19 43.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.037 α = 90 b = 88.143 β = 90 c = 119.761 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 PILATUS3 S 6M 2017-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9660 ESRF MASSIF-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 1.62 59.85 96.9 0.061 0.027 0.999 13.2 5.8 71100
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 1.62 1.66 78.2 0.91 0.582 0.487 1.2 3.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.62 59.85 70692 3451 96.233 0.202 0.2005 0.2011 0.2297 0.2302 RANDOM 25.646
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] -0.677 0.429 0.248
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.023 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_2_deg 9.587 r_dihedral_angle_other_2_deg 7.219 r_lrange_it 6.717 r_dihedral_angle_1_deg 6.708 r_lrange_other 6.649 r_scangle_it 4.807 r_scangle_other 4.807 r_mcangle_it 3.636
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.023 r_dihedral_angle_3_deg 12.703 r_dihedral_angle_2_deg 9.587 r_dihedral_angle_other_2_deg 7.219 r_lrange_it 6.717 r_dihedral_angle_1_deg 6.708 r_lrange_other 6.649 r_scangle_it 4.807 r_scangle_other 4.807 r_mcangle_it 3.636 r_mcangle_other 3.636 r_scbond_other 3.161 r_scbond_it 3.16 r_mcbond_it 2.559 r_mcbond_other 2.559 r_angle_refined_deg 1.676 r_angle_other_deg 0.587 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.218 r_nbd_other 0.187 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.116 r_chiral_restr 0.086 r_symmetry_nbtor_other 0.086 r_symmetry_xyhbond_nbd_other 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4274 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing