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Haloperidol bound D2 dopamine receptor structure inspired discovery of subtype selective ligands
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 100 mM Tris/HCl pH 7.5, 150 mM sodium malonate, 30% PEG400
Crystal Properties Matthews coefficient Solvent content 2.82 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.433 α = 90 b = 72.82 β = 90 c = 150.269 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2019-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.1 50 93.1 0.2 7.3 4.1 10160
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 1.13
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6CM4 3.1 33.386 9858 468 93.114 0.216 0.2152 0.2181 0.229 0.23 RANDOM 71.564
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] 1.871 1.617 -3.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.275 r_dihedral_angle_4_deg 17.462 r_dihedral_angle_3_deg 16.645 r_dihedral_angle_1_deg 5.592 r_chiral_restr_other 1.622 r_angle_refined_deg 1.275 r_angle_other_deg 0.601 r_nbd_other 0.223 r_nbd_refined 0.222 r_symmetry_nbd_other 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.275 r_dihedral_angle_4_deg 17.462 r_dihedral_angle_3_deg 16.645 r_dihedral_angle_1_deg 5.592 r_chiral_restr_other 1.622 r_angle_refined_deg 1.275 r_angle_other_deg 0.601 r_nbd_other 0.223 r_nbd_refined 0.222 r_symmetry_nbd_other 0.2 r_symmetry_xyhbond_nbd_other 0.183 r_symmetry_nbd_refined 0.182 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.088 r_gen_planes_refined 0.052 r_chiral_restr 0.047 r_gen_planes_other 0.045 r_bond_refined_d 0.006 r_bond_other_d 0.003 r_ext_dist_refined_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3168 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing