1DX5

Crystal structure of the thrombin-thrombomodulin complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		THROMBIN-PPACK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE

Crystal Properties
Matthews coefficient	Solvent content
2.64	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.4	α = 90
b = 214.4	β = 90
c = 131.41	γ = 120

Symmetry
Space Group	H 3

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	MARRESEARCH		1999-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

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	2.29	43.85	99.7	0.064	0.064	15.55	2.5		670680		1

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	2.3	2.42	99.7		0.216	0.169	3.87	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	THROMBIN-PPACK	2.3	10	1	98582	1964	99.7	0.2	0.2	0.241	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
x_angle_deg	1.54
x_bond_d	0.08
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13120
Nucleic Acid Atoms
Solvent Atoms	815
Heterogen Atoms	83

Software

Software
Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing