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Crystal structure of 5-HT2AR in complex with antipsychotic drug pimavanserin
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 293.15 100 mM Tris/HCl, 170 mM sodium acetate trihydrate, 32% PEG 400, 2% Polypropylene glycol P 400
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.41 α = 90 b = 54.7 β = 90 c = 179.34 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 2022-07-20 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) 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 2.6 49.41 90 0.255 0.05 0.999 9.8 32 14136
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 2.6 2.72 1.952 0.73 0.381 1.1 11.2
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 2.6 47.68 13317 777 90.04 0.24885 0.24776 0.2505 0.26834 0.2729 RANDOM 79.469
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] 1.86 5.27 -7.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.164 r_long_range_B_refined 17.049 r_long_range_B_other 17.049 r_dihedral_angle_3_deg 13.675 r_scangle_other 12.486 r_mcangle_it 10.147 r_mcangle_other 10.146 r_dihedral_angle_4_deg 9.982 r_scbond_it 8.407 r_scbond_other 8.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.164 r_long_range_B_refined 17.049 r_long_range_B_other 17.049 r_dihedral_angle_3_deg 13.675 r_scangle_other 12.486 r_mcangle_it 10.147 r_mcangle_other 10.146 r_dihedral_angle_4_deg 9.982 r_scbond_it 8.407 r_scbond_other 8.404 r_dihedral_angle_1_deg 7.174 r_mcbond_it 7.065 r_mcbond_other 7.062 r_angle_refined_deg 1.671 r_angle_other_deg 1.506 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 2794 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement XDS data scaling HKL-3000 data reduction REFMAC phasing PDB_EXTRACT data extraction