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Crystal structure of serotonin 2A receptor in complex with lisuride
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 7 293.15 100 mM Tris-HCl, 75 mM sodium acetate trihydrate, 30% (v/v) PEG400, 4% (v/v) Polypropylene glycol P 400
Crystal Properties Matthews coefficient Solvent content 2.91 57.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.08 α = 90 b = 54.51 β = 90 c = 179.04 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 2.6 48.23 95 0.996 7 13.7 14980
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 2.6 2.7 85.4 0.56 1.1 3.5
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 2.6 48.23 14156 781 94.6 0.2349 0.2338 0.2373 0.2562 0.2482 RANDOM 70.103
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] 0.81 5.28 -6.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 23.419 r_dihedral_angle_3_deg 14.073 r_mcangle_it 10.188 r_mcbond_it 7.112 r_mcbond_other 7.087 r_dihedral_angle_1_deg 6.023 r_angle_refined_deg 1.617 r_angle_other_deg 1.484 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 23.419 r_dihedral_angle_3_deg 14.073 r_mcangle_it 10.188 r_mcbond_it 7.112 r_mcbond_other 7.087 r_dihedral_angle_1_deg 6.023 r_angle_refined_deg 1.617 r_angle_other_deg 1.484 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2735 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing XDS data reduction