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Durio zibethinus trypsin inhibitor DzTI-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 0.1 M Tris-HCl, 80 mM sodium chloride, 80 mM calcium chloride, 6% PEG 8,000, 8% glycerol
Crystal Properties Matthews coefficient Solvent content 3.5 64.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.242 α = 90 b = 102.68 β = 90 c = 116.922 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 CCD RAYONIX MX-300 2021-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.35 29.68 99.9 0.094 0.101 0.038 0.999 16.2 7.3 51452 46.23
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 2.35 2.42 99.7 1.261 1.357 0.496 0.925 2.4 7.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS FREE R-VALUE 2.35 29.68 1.33 51241 2591 99.66 0.1949 0.1924 0.1931 0.2417 0.2424 55.74
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 16.4843 f_angle_d 0.9023 f_chiral_restr 0.0553 f_plane_restr 0.008 f_bond_d 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5650 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 78
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX refinement PHASER phasing