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Structure of the Full-length glucagon class B G protein-coupled receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 293 100mM HEPES, pH7.0, 300mM potassium phosphate monobasic, 25% PEG500DME, 100mM gly-gly-glycine
Crystal Properties Matthews coefficient Solvent content 3.76 73.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.61 α = 90 b = 245.33 β = 90.01 c = 96.15 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 293 PIXEL CS-PAD CXI-1 2016-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.3 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 100 4.8 198 67598
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 4L6R 3 31.78 63632 3311 99.79 0.21123 0.20953 0.1679 0.24327 0.1976 RANDOM 78.21
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] -5.16 -4.17 -8.98 14.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.224 r_dihedral_angle_3_deg 20.494 r_dihedral_angle_4_deg 16.328 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 4.643 r_long_range_B_other 4.643 r_mcangle_it 2.766 r_mcangle_other 2.766 r_scangle_other 2.055 r_mcbond_it 1.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.224 r_dihedral_angle_3_deg 20.494 r_dihedral_angle_4_deg 16.328 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 4.643 r_long_range_B_other 4.643 r_mcangle_it 2.766 r_mcangle_other 2.766 r_scangle_other 2.055 r_mcbond_it 1.537 r_mcbond_other 1.536 r_angle_refined_deg 1.414 r_scbond_it 1.114 r_scbond_other 1.114 r_angle_other_deg 1.093 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14804 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing