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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, 200mM potassium phospphate monobasic, 20% PEG500DME, 10 mM gly-gly-glysine
Crystal Properties Matthews coefficient Solvent content 3.68 66.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.46 α = 90 b = 248.79 β = 90.16 c = 93.33 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 PILATUS3 S 6M 2016-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 3.19 50 92.8 3.1 2.8 49677
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 3.19 46.92 48212 2547 94.08 0.2066 0.20526 0.1596 0.23148 0.1802 RANDOM 116.895
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] -13.93 3.56 -5.66 19.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.187 r_dihedral_angle_3_deg 19.332 r_long_range_B_refined 13.422 r_long_range_B_other 13.422 r_dihedral_angle_4_deg 12.429 r_mcangle_it 7.676 r_mcangle_other 7.675 r_scangle_other 6.98 r_dihedral_angle_1_deg 4.781 r_mcbond_it 4.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.187 r_dihedral_angle_3_deg 19.332 r_long_range_B_refined 13.422 r_long_range_B_other 13.422 r_dihedral_angle_4_deg 12.429 r_mcangle_it 7.676 r_mcangle_other 7.675 r_scangle_other 6.98 r_dihedral_angle_1_deg 4.781 r_mcbond_it 4.764 r_mcbond_other 4.764 r_scbond_it 4.259 r_scbond_other 4.258 r_angle_refined_deg 1.397 r_angle_other_deg 1.208 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 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 14762 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 278
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing