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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 281 18% W/V PEG4000, 20% V/V 2-PROPANOL,
0.2 M SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 4.16 70.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.095 α = 90 b = 94.095 β = 90 c = 124.71 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS 6M 2015-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9537 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.69 81.49 99.7 0.051 16.5 5.5 71667
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72 96.6 0.563 2 3.5
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 1HAO 1.69 81.49 68190 3441 99.54 0.14643 0.14531 0.1588 0.16832 0.1793 RANDOM 30.399
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] 0.7 0.35 0.7 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_dihedral_angle_3_deg 14.985 r_dihedral_angle_4_deg 12.475 r_long_range_B_refined 8.911 r_long_range_B_other 8.911 r_dihedral_angle_1_deg 7.833 r_scangle_other 6.622 r_mcangle_it 5.276 r_mcangle_other 5.274 r_scbond_it 4.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_dihedral_angle_3_deg 14.985 r_dihedral_angle_4_deg 12.475 r_long_range_B_refined 8.911 r_long_range_B_other 8.911 r_dihedral_angle_1_deg 7.833 r_scangle_other 6.622 r_mcangle_it 5.276 r_mcangle_other 5.274 r_scbond_it 4.568 r_scbond_other 4.567 r_mcbond_it 3.681 r_mcbond_other 3.522 r_angle_refined_deg 2.751 r_angle_other_deg 1.355 r_chiral_restr 0.176 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 Atoms Number Protein Atoms 2332 Nucleic Acid Atoms 330 Solvent Atoms 412 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing