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TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7MEQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 precipitant containing 20% PEG3350, 0.2 M dibasic ammonium citrate. Protein mixed 1uL:1uL protein:precipitant and set as 2 uL hanging drop on glass slides
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.939 α = 90 b = 172.573 β = 90 c = 83.297 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2022-06-11 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 2.19 40 99.7 0.226 0.239 0.076 0.984 5.4 9 44382
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 2.2 2.24 99.7 2.749 2.975 1.114 0.291 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.19 38.67 43904 462 99.47 0.17223 0.17168 0.22275 0.2034 RANDOM 40.183
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] -1.43 1.46 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.519 r_dihedral_angle_2_deg 9.016 r_long_range_B_refined 8.679 r_long_range_B_other 8.678 r_dihedral_angle_1_deg 7.198 r_scangle_other 6.851 r_mcangle_it 5.29 r_mcangle_other 5.289 r_scbond_it 4.73 r_scbond_other 4.729
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.519 r_dihedral_angle_2_deg 9.016 r_long_range_B_refined 8.679 r_long_range_B_other 8.678 r_dihedral_angle_1_deg 7.198 r_scangle_other 6.851 r_mcangle_it 5.29 r_mcangle_other 5.289 r_scbond_it 4.73 r_scbond_other 4.729 r_mcbond_it 3.776 r_mcbond_other 3.776 r_angle_refined_deg 1.574 r_angle_other_deg 0.518 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 5319 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 280
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing