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Crystal structure of the GFRaL receptor in complex with an inhibitory cyclic peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.3 M (NH4)2SO4, 0.1 M Na-citrate, 0.9 M LiSO4
100nL GFRaL-peptide mixture mixed with 80nL well solution and 20nL seed stock.
Crystal Properties Matthews coefficient Solvent content 2.45 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.541 α = 90 b = 148.183 β = 90 c = 198.053 γ = 90
Symmetry Space Group C 2 2 21
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 XE 16M 2019-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.980 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 99 92.5 0.999 11.2 3.5 38664
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.19 0.669
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 99 38663 1952 55.712 0.196 0.1938 0.2013 0.2445 0.247 5 33.964
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] -0.109 -0.221 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.413 r_dihedral_angle_6_deg 14.616 r_dihedral_angle_2_deg 12.302 r_lrange_it 8.731 r_lrange_other 8.709 r_dihedral_angle_1_deg 6.563 r_scangle_it 6.48 r_scangle_other 6.424 r_mcangle_it 5.047 r_mcangle_other 5.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.413 r_dihedral_angle_6_deg 14.616 r_dihedral_angle_2_deg 12.302 r_lrange_it 8.731 r_lrange_other 8.709 r_dihedral_angle_1_deg 6.563 r_scangle_it 6.48 r_scangle_other 6.424 r_mcangle_it 5.047 r_mcangle_other 5.046 r_scbond_it 4.218 r_scbond_other 4.158 r_mcbond_it 3.344 r_mcbond_other 3.339 r_angle_refined_deg 1.649 r_angle_other_deg 1.06 r_xyhbond_nbd_refined 0.423 r_symmetry_xyhbond_nbd_refined 0.245 r_nbd_other 0.24 r_nbd_refined 0.224 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.174 r_ncsr_local_group_1 0.084 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_2 0.082 r_ncsr_local_group_3 0.077 r_chiral_restr 0.075 r_bond_other_d 0.045 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4996 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing