2D1J | pdb_00002d1j

Factor Xa in complex with the inhibitor 2-[[4-[(5-chloroindol-2-yl)sulfonyl]piperazin-1-yl] carbonyl]thieno[3,2-b]pyridine n-oxide

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SEEDING	5	293	pH 5.00, VAPOR DIFFUSION, SEEDING, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.078	α = 90
b = 73.122	β = 90
c = 79.949	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	IMAGE PLATE	RIGAKU RAXIS IIC	monochromator	2000-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.2	33.25	97.3	0.055	0.055	14.6	3.57	17081	17081

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)
	2.2	2.28	95.8		0.305	0.305	4.2	3.62	1662

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	RIGID BODY REFINEMENT	THROUGHOUT	1FAX	2.2	25	16215	857	100	0.18799	0.18556	0.23219	RANDOM	38.058

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]
0.27			-0.8		0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.152
r_dihedral_angle_4_deg	25.678
r_dihedral_angle_3_deg	15.575
r_dihedral_angle_1_deg	6.59
r_scangle_it	3.724
r_mcangle_it	3.096
r_scbond_it	2.552
r_angle_refined_deg	1.953
r_mcbond_it	1.919
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.152
r_dihedral_angle_4_deg	25.678
r_dihedral_angle_3_deg	15.575
r_dihedral_angle_1_deg	6.59
r_scangle_it	3.724
r_mcangle_it	3.096
r_scbond_it	2.552
r_angle_refined_deg	1.953
r_mcbond_it	1.919
r_nbtor_refined	0.32
r_symmetry_hbond_refined	0.229
r_metal_ion_refined	0.224
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.129
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2149
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	33

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
REFMAC	refinement

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.