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Crystal structure of human TMPRSS11A S368A interacting with its own zymogen activation motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9DPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 291 1.4 M sodium/potassium phosphate pH 7.4. TMPRSS11A protein (20 mg/mL) was mixed 1:1 with precipitant (0.5 uL: 0.5 uL) using an Art Robbins Phoenix crystallization robot. Crystals were mounted with reservoir solution containing 10% ethylene glycol.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.785 α = 90 b = 81.785 β = 90 c = 44.881 γ = 90
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 EIGER X 16M 2025-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-E 0.97920 APS 21-ID-E
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 2.53 40 98.9 0.334 0.368 0.153 0.974 3.2 5.4 9798
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 2.53 2.57 95.6 1.313 1.571 0.844 0.237 2.7
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 2.54 39.38 9316 482 98.37 0.19431 0.19163 0.1979 0.24644 0.2499 RANDOM 52.118
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] 1.93 1.93 -3.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.996 r_long_range_B_refined 10.482 r_long_range_B_other 10.48 r_dihedral_angle_2_deg 8.709 r_scangle_other 8.038 r_dihedral_angle_1_deg 7.957 r_mcangle_it 6.679 r_mcangle_other 6.677 r_scbond_it 5.75 r_scbond_other 5.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.996 r_long_range_B_refined 10.482 r_long_range_B_other 10.48 r_dihedral_angle_2_deg 8.709 r_scangle_other 8.038 r_dihedral_angle_1_deg 7.957 r_mcangle_it 6.679 r_mcangle_other 6.677 r_scbond_it 5.75 r_scbond_other 5.747 r_mcbond_it 4.396 r_mcbond_other 4.393 r_angle_refined_deg 1.639 r_angle_other_deg 0.569 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 1899 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing PDB_EXTRACT data extraction