8EPK

Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
6_b4_cr4_1_1	VAPOR DIFFUSION, SITTING DROP		298	60 mM Na Citrate pH 5.0; 4% Tacsimate pH 7.0; 23% PEG 8000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.496	α = 90
b = 79.579	β = 101.78
c = 84.317	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
4	6_b4_cr4_1_1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2021-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
4	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

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
4	2.65	60.24	98.5	0.108	0.128	0.068	0.997	8.2	3.5		27106

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)
4	2.65	2.77	96.4		2.29	2.687	1.395	0.384		3.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	8EPH, 3DD2	2.65	60.24	25317	1313	96.58	0.2328	0.2313	0.2607	RANDOM	93.716

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]
0.79		-0.05	-2.16		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.266
r_dihedral_angle_3_deg	15.156
r_dihedral_angle_4_deg	10.536
r_dihedral_angle_1_deg	6.074
r_angle_refined_deg	1.759
r_angle_other_deg	1.183
r_chiral_restr	0.111
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4512
Nucleic Acid Atoms	1344
Solvent Atoms	10
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction