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High-resolution crystal structure of the human CB1 cannabinoid receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.5 293 31% PEG400, 100mM Sodium Citrate pH5.5, 100mM magnesium sulfate
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.652 α = 90 b = 80.381 β = 91.72 c = 81.178 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2016-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
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 2.6 50.01 96.9 0.194 5.6 5.4 19781
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 96.8 1.411 0.69 5.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3V2Y 2.6 50.01 11084 612 57.88 0.1832 0.1803 0.1902 0.2382 0.247 RANDOM 44.12
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] 6.05 1.27 -2.83 -3.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 18.966 r_dihedral_angle_1_deg 8.654 r_mcangle_it 6.886 r_mcbond_it 4.549 r_mcbond_other 4.547 r_angle_refined_deg 1.2 r_angle_other_deg 0.643 r_chiral_restr 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.488 r_dihedral_angle_4_deg 20.71 r_dihedral_angle_3_deg 18.966 r_dihedral_angle_1_deg 8.654 r_mcangle_it 6.886 r_mcbond_it 4.549 r_mcbond_other 4.547 r_angle_refined_deg 1.2 r_angle_other_deg 0.643 r_chiral_restr 0.249 r_gen_planes_refined 0.012 r_bond_refined_d 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3762 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 119
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing DENZO data reduction SCALEPACK data scaling