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Cystal structure of Zymogen Granule Protein 16 (ZG16)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3APA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 1.0 M ammonium sulfate, 0.1 M BIS-Tris, pH 5.5, 1 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.94 36.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.927 α = 90 b = 55.996 β = 90 c = 58.115 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2021-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
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 1.5 40.323 97.04 0.986 10.87 3.8 20346 13.97
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 1.5 1.554 97.25 0.621 3.7
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 THROUGHOUT 3APA 1.5 40.32 1.36 20346 1175 97.05 0.1732 0.1711 0.1716 0.2075 0.2079 18.4
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 2.9201 f_angle_d 0.972 f_chiral_restr 0.058 f_bond_d 0.0084 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1112 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 8
Software Software Software Name Purpose PHENIX refinement XDS data reduction HKL-2000 data scaling PDB_EXTRACT data extraction PHASER phasing