2VIP

Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.6PROTEIN WAS CRYSTALLIZED FROM 22-24% PEG4000, 0.17M (NH4)2SO4, 15% GLYCEROL, 0.1M NA(CH3COO) PH=4.0; THEN SOAKED IN 0.01M COMPOUND, 28% PEG4000, 0.29M HEPES PH=6.6, 5% GLYCEROL, 0.001M NA(CH3COO), 0.001M (NH4)2SO4, 10% DMSO
Crystal Properties
Matthews coefficientSolvent content
1.7127.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.488α = 90
b = 54.382β = 90
c = 81.029γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU CCDOSMIC BLUE CONFOCAL OPTICSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.7227.6379.60.062.520118
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)
11.721.78180.32.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONOTHERTHROUGHOUTNONE1.7227.622011899979.420.1660.16230.2375RANDOM
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1952
Nucleic Acid Atoms
Solvent Atoms387
Heterogen Atoms34

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
d*TREKdata reduction
d*TREKdata scaling