6EO6

X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(2-(1H-indol-3-yl)acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HAO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28118% W/V PEG4000, 20% V/V 2-PROPANOL, 0.2 M SODIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
4.1670.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.095α = 90
b = 94.095β = 90
c = 124.71γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9537PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6981.4999.70.05116.55.571667
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.691.7296.60.56323.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1HAO1.6981.4968190344199.540.146430.145310.16832RANDOM30.399
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]
0.70.350.7-2.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_3_deg14.985
r_dihedral_angle_4_deg12.475
r_long_range_B_refined8.911
r_long_range_B_other8.911
r_dihedral_angle_1_deg7.833
r_scangle_other6.622
r_mcangle_it5.276
r_mcangle_other5.274
r_scbond_it4.568
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_3_deg14.985
r_dihedral_angle_4_deg12.475
r_long_range_B_refined8.911
r_long_range_B_other8.911
r_dihedral_angle_1_deg7.833
r_scangle_other6.622
r_mcangle_it5.276
r_mcangle_other5.274
r_scbond_it4.568
r_scbond_other4.567
r_mcbond_it3.681
r_mcbond_other3.522
r_angle_refined_deg2.751
r_angle_other_deg1.355
r_chiral_restr0.176
r_bond_refined_d0.028
r_gen_planes_refined0.015
r_bond_other_d0.003
r_gen_planes_other0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2332
Nucleic Acid Atoms330
Solvent Atoms412
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing