6T9V

Bovine Trypsin in complex with the synthetic inhibitor (S)-3-(3-(4-(3-(tert-butyl)ureido)piperidin-1-yl)-2-((3'-fluoro-4'-(hydroxymethyl)-[1,1'-biphenyl])-3-sulfonamido)-3-oxopropyl)benzimidamide (MI-1904)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZFS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION291100 mM Imidazole pH 8.0, 100 mM Ammoniumsulfate, 20-25 % PEG8000, 0.1% Sodium-azide, 1 mM Ligand, Protein at 10-20 mg/mL
Crystal Properties
Matthews coefficientSolvent content
2.0840.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.464α = 90
b = 55.464β = 90
c = 109.142γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-05-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.126427243345099.20.0570.99918.149.4877365711.5821453576
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.131.1995.50.4970.9353.28.81

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2zfs1.1264272433443.96394334951.3758667990873647368399.18654294220.1312422139710.130165701590.15214003465516.2720204377
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d11.8216357032
f_angle_d0.961088907128
f_chiral_restr0.0843462236537
f_bond_d0.00740061070626
f_plane_restr0.00695515555333
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1616
Nucleic Acid Atoms
Solvent Atoms223
Heterogen Atoms59

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building