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Crystal structure of serotonin 2A receptor in complex with lumateperone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6A93
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8 293.15 100 mM Tris-HCl, 160 mM Potassium fluoride, 30% (v/v) PEG400
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.47 α = 90 b = 55.33 β = 90 c = 179.97 γ = 90
Symmetry Space Group P 21 2 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 2021-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 47.7 99.3 0.988 10.8 25.3 18848
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 94.1 0.422 1.1 6.6
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 6A93 2.45 47.7 17888 913 99.29 0.2197 0.2185 0.2222 0.2438 0.245 RANDOM 76.097
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] 1.46 2.19 -3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.121 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 14.562 r_mcangle_it 9.75 r_mcbond_it 7.829 r_mcbond_other 7.82 r_dihedral_angle_1_deg 5.274 r_angle_refined_deg 1.57 r_angle_other_deg 1.425 r_chiral_restr 0.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.121 r_dihedral_angle_4_deg 20.202 r_dihedral_angle_3_deg 14.562 r_mcangle_it 9.75 r_mcbond_it 7.829 r_mcbond_other 7.82 r_dihedral_angle_1_deg 5.274 r_angle_refined_deg 1.57 r_angle_other_deg 1.425 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2798 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 346
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing