6EO7

X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(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 DROP28125% W/V PEG4000, 24% V/V 2-PROPANOL, 0.2 M SODIUM CITRATE
Crystal Properties
Matthews coefficientSolvent content
4.1970.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.579α = 90
b = 94.579β = 90
c = 125.566γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
12.2447.2995.40.09115.3730342
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)
12.242.3173.40.7021.74.2

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 REPLACEMENTTHROUGHOUT1HAO2.2481.9128729158395.310.162990.160520.20848RANDOM44.27
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]
1.130.561.13-3.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.734
r_dihedral_angle_3_deg17.773
r_dihedral_angle_4_deg16.24
r_long_range_B_other11.18
r_long_range_B_refined11.147
r_scangle_other8.448
r_mcangle_other7.49
r_mcangle_it7.471
r_dihedral_angle_1_deg6.92
r_scbond_it5.622
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.734
r_dihedral_angle_3_deg17.773
r_dihedral_angle_4_deg16.24
r_long_range_B_other11.18
r_long_range_B_refined11.147
r_scangle_other8.448
r_mcangle_other7.49
r_mcangle_it7.471
r_dihedral_angle_1_deg6.92
r_scbond_it5.622
r_scbond_other5.62
r_mcbond_it4.807
r_mcbond_other4.767
r_angle_refined_deg2.306
r_angle_other_deg1.231
r_chiral_restr0.114
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms2336
Nucleic Acid Atoms321
Solvent Atoms232
Heterogen Atoms46

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement