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Crystal structure of TMPRSS11D S368A complexed with its own zymogen activation motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8VIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.5M Mg form, 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.034 α = 90 b = 76.64 β = 90 c = 88.374 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 EIGER2 X 16M 2024-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 1.033 CLSI 08ID-1
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 1.9 40 99.2 0.183 0.192 0.056 0.984 3.6 11.4 37404
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 1.98 2.01 99.7 1.308 1.38 0.426 0.817 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.9 38.31 37404 1976 99.19 0.20141 0.19868 0.2085 0.25411 0.2574 RANDOM 30.976
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] 3.31 0.95 -4.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.267 r_long_range_B_refined 7.461 r_long_range_B_other 7.461 r_dihedral_angle_2_deg 7.068 r_dihedral_angle_1_deg 7.024 r_scangle_other 5.806 r_scbond_it 3.889 r_scbond_other 3.888 r_mcangle_other 3.646 r_mcangle_it 3.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.267 r_long_range_B_refined 7.461 r_long_range_B_other 7.461 r_dihedral_angle_2_deg 7.068 r_dihedral_angle_1_deg 7.024 r_scangle_other 5.806 r_scbond_it 3.889 r_scbond_other 3.888 r_mcangle_other 3.646 r_mcangle_it 3.645 r_mcbond_it 2.646 r_mcbond_other 2.646 r_angle_refined_deg 1.522 r_angle_other_deg 0.518 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3780 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing