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High resolution TMPRSS2 structure following acylation by nafamostat
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 3 uL hanging drop (2:1 protein:precipitant) grown over precipitant solution containing 25%PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate pH 4.6. Protein (10 mg/mL) was in a buffer containing 25 mM Tris pH 8.0, 75 mM NaCl, and 2 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.757 α = 90 b = 50.502 β = 91.6 c = 64.578 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2022-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 1.58 40 92.8 0.099 0.127 0.079 0.988 8.7 2.2 94364
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 1.58 1.61 91.6 0.663 0.851 0.528 0.625 2.2
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 1.58 39.81 49216 2463 99 0.15695 0.15571 0.1678 0.18084 0.188 RANDOM 19.803
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] 2.51 0.88 -0.25 -2.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.824 r_dihedral_angle_2_deg 7.446 r_long_range_B_refined 6.889 r_long_range_B_other 6.887 r_dihedral_angle_1_deg 6.732 r_scangle_other 4.64 r_mcangle_other 3.125 r_mcangle_it 3.123 r_scbond_it 3.113 r_scbond_other 3.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.824 r_dihedral_angle_2_deg 7.446 r_long_range_B_refined 6.889 r_long_range_B_other 6.887 r_dihedral_angle_1_deg 6.732 r_scangle_other 4.64 r_mcangle_other 3.125 r_mcangle_it 3.123 r_scbond_it 3.113 r_scbond_other 3.112 r_mcbond_it 2.079 r_mcbond_other 2.077 r_angle_refined_deg 1.659 r_angle_other_deg 0.596 r_chiral_restr 0.085 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 2614 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing