7WC9

Crystal structure of serotonin 2A receptor in complex with non-hallucinogenic psychedelic analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6A93 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293.15100 mM Tris-HCl, 40 mM sodium acetate trihydrate, 30% (v/v) PEG400, 2% (v/v) Polypropylene glycol P 400
Crystal Properties
Matthews coefficientSolvent content
2.9157.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.53α = 90
b = 54.95β = 90
c = 179.88γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1SPring-8BL45XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.547.810019.925.121037
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.699.90.390.910.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6A932.547.81678194199.950.24510.2440.2656RANDOM72.295
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]
1.93.85-5.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.493
r_dihedral_angle_4_deg15.393
r_dihedral_angle_3_deg14.307
r_mcangle_it8.968
r_mcbond_other6.35
r_mcbond_it6.349
r_dihedral_angle_1_deg5.599
r_angle_refined_deg1.493
r_angle_other_deg1.39
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.493
r_dihedral_angle_4_deg15.393
r_dihedral_angle_3_deg14.307
r_mcangle_it8.968
r_mcbond_other6.35
r_mcbond_it6.349
r_dihedral_angle_1_deg5.599
r_angle_refined_deg1.493
r_angle_other_deg1.39
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2735
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms236

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASESphasing