7WC5

Crystal structure of serotonin 2A receptor in complex with psilocin


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, 175 mM sodium acetate trihydrate, 30% (v/v) PEG400, 4% (v/v) Polypropylene glycol P 400
Crystal Properties
Matthews coefficientSolvent content
2.8857.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.07α = 90
b = 54.33β = 90
c = 178.33γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-10-21MSINGLE 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
13.248.2197.30.9924.99.28348
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)
13.23.3185.70.27513.2

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 REPLACEMENTTHROUGHOUT6A933.248.21790741097.230.2340.23270.2572RANDOM73.042
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]
1.753.5-5.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.984
r_dihedral_angle_3_deg14.921
r_dihedral_angle_4_deg13.394
r_mcangle_it13.125
r_mcbond_it8.91
r_mcbond_other8.81
r_dihedral_angle_1_deg7.171
r_angle_refined_deg1.805
r_angle_other_deg1.518
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.984
r_dihedral_angle_3_deg14.921
r_dihedral_angle_4_deg13.394
r_mcangle_it13.125
r_mcbond_it8.91
r_mcbond_other8.81
r_dihedral_angle_1_deg7.171
r_angle_refined_deg1.805
r_angle_other_deg1.518
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2773
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing
XDSdata reduction