2A45

Crystal structure of the complex between thrombin and the central "E" region of fibrin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PPB	PDB entries 1PPB, 1JY2
experimental model	PDB	1JY2	PDB entries 1PPB, 1JY2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7.9	298	PEG 3500, AMMONIUM PHOSPHATE, TRIS, pH 7.90, MICRODIALYSIS, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.89	55.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.263	α = 90
b = 76.263	β = 90
c = 192.452	γ = 120

Symmetry
Space Group	P 31

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	COLLIMATOR		M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.65	31.24	96.3	3.4			26890

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.65	3.78	87.6		1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entries 1PPB, 1JY2	3.65	19.7	25847	2390	93.4	0.221		0.29	RANDOM

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
s_bond_d	0.013
s_angle_d
s_similar_dist
s_from_restr_planes
s_zero_chiral_vol
s_non_zero_chiral_vol
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_similar_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6834
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	70

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
CNS	refinement
SHELXL-97	refinement
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 R01GM133198.