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Crystal structure of human secretory glutaminyl cyclase in complex with the inhibitor N-(1H-benzo[d]imidazol-5-yl)-1-phenylmethanesulfonamide (compound 5)
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 2.72 54.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.54 α = 96.21 b = 116.476 β = 114.92 c = 122.75 γ = 109.69
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 2024-07-01 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 2.184 39.212 97.84 0.3243 0.3912 0.215 0.1964 4.95 3.33 262894
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 2.184 2.24 1.8774 2.2845 1.2764 0.0903 0.49
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 2.367 39.212 1.96 208064 1585 98.57 0.1897 0.1891 0.1906 0.2621 0.2632
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 16.496 f_angle_d 1.801 f_chiral_restr 0.081 f_bond_d 0.024 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31320 Nucleic Acid Atoms Solvent Atoms 1407 Heterogen Atoms 309
Software Software Software Name Purpose PHENIX refinement autoPX data processing autoPX data reduction PHENIX phasing