7VOE

Crystal structure of 5-HT2AR in complex with aripiprazole


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, 50 mM ammonium floride, 28%-30% PEG400, 300 mM NDSB-195 or 3% w/v trimethylamine N-oxide dihydrate
Crystal Properties
Matthews coefficientSolvent content
2.9257.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.27α = 90
b = 54.28β = 90
c = 179.55γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-07-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1SPring-8BL45XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.948.4198.90.2580.260.030.99813.453.611410
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.93.0894.31.5261.5930.4430.651.39.7

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 REPLACEMENTTHROUGHOUT6A932.948.411078358998.80.22370.22270.2437RANDOM70.901
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]
1.515.22-6.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.197
r_dihedral_angle_3_deg16.039
r_dihedral_angle_4_deg12.808
r_mcangle_it10.664
r_mcbond_other7.23
r_mcbond_it7.229
r_dihedral_angle_1_deg6.149
r_angle_refined_deg1.685
r_angle_other_deg1.365
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.197
r_dihedral_angle_3_deg16.039
r_dihedral_angle_4_deg12.808
r_mcangle_it10.664
r_mcbond_other7.23
r_mcbond_it7.229
r_dihedral_angle_1_deg6.149
r_angle_refined_deg1.685
r_angle_other_deg1.365
r_chiral_restr0.076
r_bond_refined_d0.01
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 Atoms2718
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms201

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing