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Crystal structure of human secretory glutaminyl cyclase in complex with the inhibitor 3-((2-(1H-imidazol-5-yl)ethyl)carbamoyl)-4-amino-1,2,5-oxadiazole 2-oxide (compound 13)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 12-16% (v/v) polyethylene glycol 4000, 0.2 M MgCl2 and 0.1 M Tris-HCl at pH 8.5.
Crystal Properties Matthews coefficient Solvent content 5.84 78.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 274.6 α = 90 b = 274.6 β = 90 c = 274.6 γ = 90
Symmetry Space Group F 41 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 195 PIXEL DECTRIS PILATUS3 6M 2024-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97946 SSRF BL18U1
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 2.96 34.33 99.9 0.56 0.564 0.064 0.997 12.3 76.7 19047
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 2.96 3.04 100 4.906 4.937 0.549 0.628 80.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3PBB 2.961 34.325 1.34 19022 1903 99.97 0.2109 0.206 0.2125 0.2552 0.2539
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.121 f_angle_d 1.325 f_chiral_restr 0.077 f_bond_d 0.023 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2610 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PHENIX phasing XDS data reduction