6LUQ

Haloperidol bound D2 dopamine receptor structure inspired discovery of subtype selective ligands


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6CM4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE293100 mM Tris/HCl pH 7.5, 150 mM sodium malonate, 30% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.8256.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.433α = 90
b = 72.82β = 90
c = 150.269γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS3 6M2019-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.15093.10.27.34.110160
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.21.13

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6CM43.133.386985846893.1140.2160.21520.229RANDOM71.564
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]
1.8711.617-3.488
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.275
r_dihedral_angle_4_deg17.462
r_dihedral_angle_3_deg16.645
r_dihedral_angle_1_deg5.592
r_chiral_restr_other1.622
r_angle_refined_deg1.275
r_angle_other_deg0.601
r_nbd_other0.223
r_nbd_refined0.222
r_symmetry_nbd_other0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.275
r_dihedral_angle_4_deg17.462
r_dihedral_angle_3_deg16.645
r_dihedral_angle_1_deg5.592
r_chiral_restr_other1.622
r_angle_refined_deg1.275
r_angle_other_deg0.601
r_nbd_other0.223
r_nbd_refined0.222
r_symmetry_nbd_other0.2
r_symmetry_xyhbond_nbd_other0.183
r_symmetry_nbd_refined0.182
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.174
r_symmetry_xyhbond_nbd_refined0.104
r_symmetry_nbtor_other0.088
r_gen_planes_refined0.052
r_chiral_restr0.047
r_gen_planes_other0.045
r_bond_refined_d0.006
r_bond_other_d0.003
r_ext_dist_refined_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3168
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing