8TQS

Complex of human thrombin (S195A) bound to a bivalent inhibitor comprised of DNA Aptamer HD22 conjugated to Dabigatran with a linker.

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	0.1 M MES monohydrate pH 6, 22% (v/v) polyethylene glycol 400 (Hampton PEGRx1 #08)

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.626	α = 90
b = 81.626	β = 90
c = 190.514	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2022-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.979354	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.2	41.2	100	0.153	0.159	0.042	0.99	8.9	14.4		33265

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.21	5.99	100		5.615	5.808	1.473	0.4		15.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.207	41.138	33010	1999	99.23	0.216	0.2138	0.2446	RANDOM	80.055

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]
-0.805			-0.805		1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.259
r_dihedral_angle_3_deg	13.161
r_lrange_other	11.889
r_lrange_it	11.886
r_scangle_it	7.576
r_scangle_other	7.575
r_dihedral_angle_1_deg	6.705
r_scbond_it	4.994
r_scbond_other	4.993
r_dihedral_angle_2_deg	4.746
r_mcangle_it	4.39
r_mcangle_other	4.39
r_mcbond_it	3.03
r_mcbond_other	3.028
r_angle_refined_deg	1.066
r_dihedral_angle_other_2_deg	0.585
r_angle_other_deg	0.347
r_xyhbond_nbd_refined	0.256
r_symmetry_nbd_other	0.194
r_nbd_refined	0.193
r_nbtor_refined	0.193
r_nbd_other	0.178
r_symmetry_nbd_refined	0.107
r_metal_ion_refined	0.095
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.047
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2371
Nucleic Acid Atoms	629
Solvent Atoms	14
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data scaling
XDS	data reduction
PHASER	phasing