7WC8

Crystal structure of serotonin 2A receptor in complex with lumateperone


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE8293.15100 mM Tris-HCl, 160 mM Potassium fluoride, 30% (v/v) PEG400
Crystal Properties
Matthews coefficientSolvent content
2.9358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.47α = 90
b = 55.33β = 90
c = 179.97γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-02-03MSINGLE 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
12.4547.799.30.98810.825.318848
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)
12.452.5494.10.4221.16.6

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 REPLACEMENTTHROUGHOUT6A932.4547.71788891399.290.21970.21850.2438RANDOM76.097
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]
1.462.19-3.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.121
r_dihedral_angle_4_deg20.202
r_dihedral_angle_3_deg14.562
r_mcangle_it9.75
r_mcbond_it7.829
r_mcbond_other7.82
r_dihedral_angle_1_deg5.274
r_angle_refined_deg1.57
r_angle_other_deg1.425
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.121
r_dihedral_angle_4_deg20.202
r_dihedral_angle_3_deg14.562
r_mcangle_it9.75
r_mcbond_it7.829
r_mcbond_other7.82
r_dihedral_angle_1_deg5.274
r_angle_refined_deg1.57
r_angle_other_deg1.425
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2798
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms346

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing