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Crystal structure of an inverse agonist antipsychotic drug pimavanserin-bound 5-HT2A
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 6 293 32-38%PEG300, 40-60mM lithium chloride
Crystal Properties Matthews coefficient Solvent content 2.81 56.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 276.26 α = 90 b = 42.04 β = 93.147 c = 90.41 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 PILATUS 6M 2022-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.4 45.14 99.9 1.231 1.246 0.2694 0.982 6.7 20.7 14824 82.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.61 3.091 3.131 0.6797 0.584
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6A93 3.4 45.14 1.34 14774 1470 99.66 0.2943 0.2907 0.2907 0.3277 0.326 104.82
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.3041 f_angle_d 0.5136 f_chiral_restr 0.0364 f_plane_restr 0.0049 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5707 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction PHENIX phasing