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Crystal structure of an acylated GLP-1/GIP analogue peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QKH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 298 0.1M sodium citrate pH 4.5, 0.2M ammonium phosphate monobasic, 0.1M ammonium sulfate, 32% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.95 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.66 α = 90 b = 64.66 β = 90 c = 11.417 γ = 90
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 EIGER2 S 9M 2024-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.62 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.59 64.66 99.8 0.269 0.318 0.169 0.988 3.8 6.3 6855
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.59 1.62 100 2.936 3.48 1.85 0.173 0.7 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.59 64.66 6852 674 99.767 0.212 0.2083 0.2163 0.245 0.2562 24.604
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] -1.187 -1.187 2.373
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.065 r_lrange_other 17.74 r_dihedral_angle_3_deg 15.141 r_dihedral_angle_6_deg 13.807 r_scangle_it 10.577 r_scangle_other 10.554 r_mcangle_other 9.335 r_mcangle_it 9.279 r_scbond_it 7.351 r_scbond_other 7.329
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.065 r_lrange_other 17.74 r_dihedral_angle_3_deg 15.141 r_dihedral_angle_6_deg 13.807 r_scangle_it 10.577 r_scangle_other 10.554 r_mcangle_other 9.335 r_mcangle_it 9.279 r_scbond_it 7.351 r_scbond_other 7.329 r_rigid_bond_restr 6.172 r_mcbond_it 6.069 r_mcbond_other 5.903 r_dihedral_angle_1_deg 5.681 r_angle_refined_deg 2.05 r_angle_other_deg 0.776 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.218 r_nbtor_refined 0.197 r_nbd_other 0.16 r_xyhbond_nbd_refined 0.156 r_symmetry_nbd_other 0.155 r_symmetry_xyhbond_nbd_refined 0.148 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 255 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 20
Software Software Software Name Purpose DIALS data reduction xia2 data reduction Aimless data scaling MrBUMP phasing BUCCANEER model building Coot model building REFMAC refinement