Experiment: 3CVM

High resolution structure of a stable Plasminogen activator inhibitor type-1 in its protease cleaved form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9PAI	PDB ENTRY 9PAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.1M Tris, 4.5M Ammonium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.603	α = 90
b = 104.014	β = 101.93
c = 76.426	γ = 90

Symmetry
Space Group	P 1 21 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		2007-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	2.02	20	97.8	0.127	9.31	3.2	76809	75140		-3	34.051

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)
	2.02	2.1	98.6		0.551	2.5	3.2	8364

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 9PAI	2.02	19.635	75139	2255	97.98	0.229	0.228	0.2318	0.282	0.2817	Random	25.49

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]
-2.447		14.184	-2.9		5.348

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.402
f_angle_d	0.813
f_chiral_restr	0.063
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11984
Nucleic Acid Atoms
Solvent Atoms	810
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing