7NTU | pdb_00007ntu

X-ray structure of the complex between human alpha thrombin and two duplex/quadruplex aptamers: NU172 and HD22_27mer

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, HANGING DROP	6.5	293	26% w/v PEG 3350, 0.2 M ammonium acetate and 0.1 M Bis-Tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.87	60.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.927	α = 90
b = 77.616	β = 103.47
c = 95.408	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
1	1	x-ray	100	CCD	RIGAKU SATURN 944		2018-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3.1	60	99.8	1	6.6	3.7		22065

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.1	3.21	99.8		0.8	2.2	3.7

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1PPB	3.1	26.77	20946	1089	99.32	0.2027	0.1999	0.21	0.257	0.26	RANDOM	36.82

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]
2.73		-1.67	-4.28		2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.393
r_dihedral_angle_3_deg	10.056
r_dihedral_angle_4_deg	8.919
r_dihedral_angle_1_deg	2.589
r_angle_other_deg	1.138
r_angle_refined_deg	1.067
r_chiral_restr	0.05
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	16.393
r_dihedral_angle_3_deg	10.056
r_dihedral_angle_4_deg	8.919
r_dihedral_angle_1_deg	2.589
r_angle_other_deg	1.138
r_angle_refined_deg	1.067
r_chiral_restr	0.05
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4462
Nucleic Acid Atoms	2214
Solvent Atoms	53
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

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.