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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 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer (HEPES), pH 7.0, 30 % v/v Jeffamine ED-2003
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.336 α = 90 b = 58.336 β = 90 c = 82.618 γ = 120
Symmetry Space Group P 32 2 1
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 2021-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9731 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.08 43.101 99.04 0.03997 0.999 11.6 3.1 69590 13.67
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 1.08 1.119 99.58 0.411 3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3APA 1.08 43.1 1.07 124616 3207 92.34 0.1648 0.1645 0.1748 0.1839 18.25
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 3.165 f_angle_d 0.9774 f_chiral_restr 0.0784 f_bond_d 0.0065 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1085 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction XDS data scaling PHASER phasing