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GluN1b-GluN2B ATD in complex with radiprodil
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 291.15 4 M sodium formate, 0.1 M HEPES (pH 7.5), 35 mM NaCl, 7 mM Tris (pH 8.0)
Crystal Properties Matthews coefficient Solvent content 3.26 62.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 267.949 α = 90 b = 60.672 β = 116.23 c = 144.647 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 NSLS-II BEAMLINE 17-ID-1 0.920126 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.74 30 98.8 0.07 0.996 10.7 4.1 52067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.74 2.81 0.781
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 (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 2.74 25 52067 2653 98.36 0.18827 0.18652 0.2335 0.22276 0.262 RANDOM 41.375
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] 0.45 1.55 -4.66 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.686 r_dihedral_angle_4_deg 14.756 r_dihedral_angle_3_deg 12.945 r_long_range_B_refined 10.951 r_long_range_B_other 10.937 r_scangle_other 7.031 r_mcangle_it 6.021 r_mcangle_other 6.02 r_scbond_it 4.7 r_scbond_other 4.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.686 r_dihedral_angle_4_deg 14.756 r_dihedral_angle_3_deg 12.945 r_long_range_B_refined 10.951 r_long_range_B_other 10.937 r_scangle_other 7.031 r_mcangle_it 6.021 r_mcangle_other 6.02 r_scbond_it 4.7 r_scbond_other 4.662 r_dihedral_angle_1_deg 4.208 r_mcbond_it 4 r_mcbond_other 4 r_angle_refined_deg 0.654 r_angle_other_deg 0.499 r_chiral_restr 0.039 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11056 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction