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Crystal structure of serotonin 2A receptor in complex with serotonin
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 , 100 mM sodium acetate trihydrate, 30% (v/v) polyethylene glycol 400 (PEG400), 4% (v/v) Polypropylene glycol P 400
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.9 α = 90 b = 54.73 β = 90 c = 178.02 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 2020-10-21 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 3.2 48.05 99 0.996 5.2 9.1 8511
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 3.2 3.31 96.6 0.323 1 6.4
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 3.2 48.05 8038 441 98.88 0.2339 0.2324 0.2339 0.2606 0.2648 RANDOM 71.165
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] 0.22 5.25 -5.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.056 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 14.435 r_mcangle_it 12.229 r_mcbond_other 7.988 r_mcbond_it 7.987 r_dihedral_angle_1_deg 7.226 r_angle_refined_deg 1.739 r_angle_other_deg 1.499 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.056 r_dihedral_angle_4_deg 15.753 r_dihedral_angle_3_deg 14.435 r_mcangle_it 12.229 r_mcbond_other 7.988 r_mcbond_it 7.987 r_dihedral_angle_1_deg 7.226 r_angle_refined_deg 1.739 r_angle_other_deg 1.499 r_chiral_restr 0.08 r_bond_refined_d 0.01 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 2824 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 145
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing XDS data reduction