Crystal structure of the thrombin-thrombomodulin complex

entry_id	1dx5
deposition_date	1999-12-20
title	Crystal structure of the thrombin-thrombomodulin complex
keywords	SERINE PROTEINASE, EGF-LIKE DOMAINS, ANTICOAGULANT COMPLEX, ANTIFIBRINOLYTIC COMPLEX, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
method	X-RAY DIFFRACTION

rg_guinier	45.29 Å
rg_electron	45.20 Å
i0	1067600000.00
molecular_weight	176080.0 kDa
excluded_volume	168720 ų
envelope_volume	345440 ų
shell_volume	65149 ų
envelope_diameter	189.3 Å
shell_rg	48.09 Å
envelope_rg	45.26 Å
shape_rg	45.10 Å
total_rg	45.45 Å
total_atoms	13203
n_residues	1652
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	179.4 Å
rg_real	45.42 Å
rg_real_error	2.28 Å
i0_real	1.0680e+09
i0_real_error	2.0490e+07
rg_reciprocal	45.29 Å
i0_reciprocal	1067000000.0000
total_estimate	0.8043
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	56.4 Å
skewness	0.417
kurtosis	-0.082
angular_range	— – 0.1750 Å−1
current_alpha	0.0000
highest_alpha	53310000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.559; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.782; Smooth: 0.994

Unit Cell

length_a	214.400 Å
length_b	214.400 Å
length_c	131.410 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	36

Symmetry

space_group	H 3
int_tables_number	146
crystal_system	—

Refinement

resolution	2.300 Å
resolution_low	10.000 Å
r_factor	0.2000
r_work	0.2000
r_free	0.2410

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/dx/1dx5/pr_distribution.json
• pr_output /app/data/pr_computation/dx/1dx5/1dx5.pr.out
• pr_plot /app/data/visualization/pr_computation/dx/1dx5/1dx5_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/dx/1dx5/1dx5.dat
• saxs_fit /app/data/saxs_computation/dx/1dx5/1dx5.fit
• saxs_log /app/data/saxs_computation/dx/1dx5/1dx5.log
• saxs_plot /app/data/visualization/saxs_computation/dx/1dx5/1dx5_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/dx/1dx5/1dx5.fit
pddf	/app/data/pr_computation/dx/1dx5/1dx5.pr.out
profile	/app/data/saxs_computation/dx/1dx5/1dx5.dat