1C5L

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

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.2		Thrombin was purchased from Haematologic Technologies, Inc. and acetyl-hirudin from Bachem. Thrombin was prepared as described (Skrzpczak-Jankun et al., 1991). Thrombin (1.0 mg/ml in 50 mM HEPES, 50 % glycerol, pH 7.0) was incubated with 1.0 mM acetyl-hirudin for 1 hr at 4 deg C. Glycerol was removed and the complex concentrated with a centricon 10 (Amicon) to about 10 mg/ml as determined by the Biorad protein assay kit using bovine serum albumin. Crystals of thrombin-acetyl-hirudin were grown in hanging drops by vapor diffusion after streak seeding. The drops were made from 5 microliters of complex and 5 microliters of reservoir solution (0.10 M Tris, 0.50 M NaCl, 22 % (by volume) PEG 4K, pH 8.20)., VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
2.74	36.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.37	α = 90
b = 73.52	β = 100.93
c = 73.85	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IV++	MSC MIRRORS	1999-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.31	44.16	69	0.071	9.8	2.2	51674			0.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.47	1.54	35.8		0.371	1.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER PLUS REFINEMENT	X-PLOR	1.47	7.5	1.8	36792	4433	69	0.215	0.215	0.236

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
Key	Refinement Restraint Deviation
x_dihedral_angle_d	25.5
x_angle_deg	3.9
x_improper_angle_d	0.47
x_bond_d	0.019

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2421
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	2

Software

Software
Software Name	Purpose
bioteX	data collection
bioteX	data reduction
X-PLOR	model building
Quanta	model building
Insight II	model building
X-PLOR	refinement
bioteX	data scaling
X-PLOR	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.