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Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 N34S (SPINK1 N34S)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CGI 1TRN_A, 1CGI_I experimental model PDB 1TRN 1TRN_A, 1CGI_I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 1 uL protein solution (20 mg/mL in 20 mM Hepes pH 7.4, 150 mM NaCl) + 1 uL well solution (15% PEG 4000, 0.3 M AS), cryo: 15% PEG 4000, 0.3 M AS, 8% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.71 54.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.555 α = 90 b = 76.555 β = 90 c = 189.719 γ = 120
Symmetry Space Group P 31 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 PILATUS3 S 2M DCM Si(111) 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.1 50 99.8 0.174 0.179 0.999 14.8 19.7 38593 -3 50.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.22 98.7 3.172 3.256 0.411 1 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1TRN_A, 1CGI_I 2.1 50 38518 1899 99.974 0.195 0.1927 0.1905 0.2336 0.232 50.032
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] 0.174 0.087 0.174 -0.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.453 r_dihedral_angle_4_deg 21.506 r_dihedral_angle_3_deg 17.006 r_dihedral_angle_1_deg 7.786 r_lrange_it 6.422 r_lrange_other 6.402 r_scangle_it 3.804 r_scangle_other 3.759 r_mcangle_it 2.727 r_mcangle_other 2.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.453 r_dihedral_angle_4_deg 21.506 r_dihedral_angle_3_deg 17.006 r_dihedral_angle_1_deg 7.786 r_lrange_it 6.422 r_lrange_other 6.402 r_scangle_it 3.804 r_scangle_other 3.759 r_mcangle_it 2.727 r_mcangle_other 2.727 r_scbond_it 2.548 r_scbond_other 2.52 r_mcbond_it 1.889 r_mcbond_other 1.889 r_angle_refined_deg 1.838 r_angle_other_deg 1.354 r_symmetry_nbd_refined 0.266 r_nbd_other 0.226 r_symmetry_xyhbond_nbd_refined 0.226 r_nbd_refined 0.194 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.165 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_symmetry_xyhbond_nbd_other 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4241 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing