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Human TMPRSS11D complexed with a disulfide-linked autoinhibitory DDDDK peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQ5 catalytic chain obtained by MR. Stem chain manually built.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.5 uL protein (30 mg/mL; in 50 mM Tris pH 8.0, 200 mM NaCl) mixed 1:1 with precipitant (20%PEG1500, 0.2M MgCl2, 0.1M HEPES pH 7.5) through automated addition with Art Robbin Phoenix robot.
Crystal Properties Matthews coefficient Solvent content 1.94 36.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.676 α = 90 b = 119.676 β = 90 c = 134.289 γ = 90
Symmetry Space Group P 43 21 2
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 2023-07-28 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 1.59 50 99.8 0.233 0.261 0.115 0.954 6.5 4.8 129049
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 2.39 2.43 99.7 2.004 2.256 1.025 0.269 4.3
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 1.59 49.77 129049 1331 99.99 0.15535 0.15502 0.1677 0.1874 0.1951 RANDOM 14.466
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] -0.11 -0.11 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.489 r_dihedral_angle_2_deg 10.265 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 5.813 r_long_range_B_other 5.588 r_scangle_other 3.983 r_scbond_it 2.633 r_scbond_other 2.631 r_mcangle_other 2.394 r_mcangle_it 2.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.489 r_dihedral_angle_2_deg 10.265 r_dihedral_angle_1_deg 6.595 r_long_range_B_refined 5.813 r_long_range_B_other 5.588 r_scangle_other 3.983 r_scbond_it 2.633 r_scbond_other 2.631 r_mcangle_other 2.394 r_mcangle_it 2.393 r_angle_refined_deg 1.611 r_mcbond_it 1.571 r_mcbond_other 1.568 r_angle_other_deg 0.566 r_chiral_restr 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 7732 Nucleic Acid Atoms Solvent Atoms 1149 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing