8V04

High resolution TMPRSS2 structure following acylation by nafamostat


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6KD5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62913 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 coefficientSolvent content
2.5251.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.757α = 90
b = 50.502β = 91.6
c = 64.578γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.584092.80.0990.1270.0790.9888.72.294364
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)RedundancyNumber Unique Reflections (All)
11.581.6191.60.6630.8510.5280.6252.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5839.81492162463990.156950.155710.18084RANDOM19.803
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]
2.510.88-0.25-2.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.824
r_dihedral_angle_2_deg7.446
r_long_range_B_refined6.889
r_long_range_B_other6.887
r_dihedral_angle_1_deg6.732
r_scangle_other4.64
r_mcangle_other3.125
r_mcangle_it3.123
r_scbond_it3.113
r_scbond_other3.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.824
r_dihedral_angle_2_deg7.446
r_long_range_B_refined6.889
r_long_range_B_other6.887
r_dihedral_angle_1_deg6.732
r_scangle_other4.64
r_mcangle_other3.125
r_mcangle_it3.123
r_scbond_it3.113
r_scbond_other3.112
r_mcbond_it2.079
r_mcbond_other2.077
r_angle_refined_deg1.659
r_angle_other_deg0.596
r_chiral_restr0.085
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms2614
Nucleic Acid Atoms
Solvent Atoms320
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing