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TMPRSS2 crystal structure following acylation by UCSF_157
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8V04
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 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.853 α = 90 b = 51.392 β = 91.01 c = 64.625 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 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 2.06 40 96.3 0.233 0.259 0.11 0.93 4.1 5.1 23755
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 2.06 2.1 86.1 0.942 1.061 0.476 0.548 4.1
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 2.07 39.29 22613 1128 96.21 0.20294 0.20004 0.2087 0.25991 0.265 RANDOM 35.376
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] 4.65 1.27 -2.81 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.239 r_long_range_B_refined 8.208 r_long_range_B_other 8.207 r_dihedral_angle_1_deg 7.76 r_dihedral_angle_2_deg 5.995 r_scangle_other 5.975 r_mcangle_other 5.067 r_mcangle_it 5.06 r_scbond_other 4.055 r_scbond_it 4.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.239 r_long_range_B_refined 8.208 r_long_range_B_other 8.207 r_dihedral_angle_1_deg 7.76 r_dihedral_angle_2_deg 5.995 r_scangle_other 5.975 r_mcangle_other 5.067 r_mcangle_it 5.06 r_scbond_other 4.055 r_scbond_it 4.054 r_mcbond_it 3.51 r_mcbond_other 3.454 r_angle_refined_deg 1.501 r_angle_other_deg 0.539 r_chiral_restr 0.075 r_bond_refined_d 0.008 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 2436 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing