1LK6 | pdb_00001lk6

Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JVQ	Dimeric antithrombin complexed with a P14-P8 reactive loop peptide and an exogenous tetrapeptide (1jvq). Both peptides omitted in starting model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	PEG 4000, sodium cacodylate, ammonium fluoride, glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 298K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.811	α = 90
b = 99.908	β = 104.44
c = 87.292	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	ADSC QUANTUM 4	mirrors	2002-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	0.978	SRS	PX14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	37.58	96.7	0.104	0.087	7.5	3.3	27398	27376		-3.7	51.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	81.5		0.551	0.431	1.7	2.5	3351

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Dimeric antithrombin complexed with a P14-P8 reactive loop peptide and an exogenous tetrapeptide (1jvq). Both peptides omitted in starting model	2.8	34.03	28306	27351	1374	96.6	0.202	0.2	0.266	0.26	Random	55.26

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]
-0.54		-5.53	9.09		-8.56

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23
c_angle_deg	1.3
c_improper_angle_d	0.81
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6603
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	126

Software

Software
Software Name	Purpose
MOSFLM	data reduction
TRUNCATE	data reduction
CNS	refinement
CCP4	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.