1C5Q

STRUCTURAL BASIS FOR SELECTIVITY OF A SMALL MOLECULE, S1-BINDING, SUB-MICROMOLAR INHIBITOR OF UROKINASE TYPE PLASMINOGEN ACTIVATOR


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.2trypsin-benzamidine, P2(1)2(1)2(1) were grown by vapor diffusion, as described for P2(1) 2(1) 2(1) (large cell) (Mangel, et al., Biochemistry 29, 8351-8357, 1990) The crystal was soaked in a solution of 85 % MgSO4 . 7 H2O, 1 mM CaCl2, 2.0 % DMSO, saturated with inhibitor, 100 mM Tris, pH 8.20 over a period of several days with several replacements of the soaking solution.
Crystal Properties
Matthews coefficientSolvent content
3.0544.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.87α = 90
b = 64.11β = 90
c = 69.49γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IV++MSC MIRRORS1997-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.3331.93750.08710.92.1415271
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.431.4939.10.2592.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONDIFFERENCE FOURIER PLUS REFINEMENTX-PLOR1.437.52396553987750.1970.1970.221
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
x_dihedral_angle_d26.2
x_angle_deg3.8
x_improper_angle_d0.54
x_bond_d0.018
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3366
Nucleic Acid Atoms
Solvent Atoms735
Heterogen Atoms23

Software

Software
Software NamePurpose
bioteXdata collection
bioteXdata reduction
X-PLORmodel building
Quantamodel building
Insight IImodel building
X-PLORrefinement
bioteXdata scaling
X-PLORphasing