4G8R

Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.963	α = 90
b = 65.504	β = 100.62
c = 96.99	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	100	CCD	MARMOSAIC 300 mm CCD	mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.97872	APS	21-ID-D

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	2.19	50	99.9	0.095	10.7	7.2	42775	42733		-3	33.27

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	2.2	2.24	99.4		0.367		6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.19	38.58	42703	2157	99.15	0.1773	0.1753	0.2148	RANDOM	36.12

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]
7.4398		1.4695	2.7236		-10.1634

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	3.67
t_other_torsion	2.81
t_angle_deg	1.06
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

RMS Deviations
Key	Refinement Restraint Deviation
t_omega_torsion	3.67
t_other_torsion	2.81
t_angle_deg	1.06
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5739
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	87

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

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.