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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
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 25% W/V PEG4000, 24% V/V 2-PROPANOL,
0.2 M SODIUM CITRATE
Crystal Properties Matthews coefficient Solvent content 4.19 70.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.579 α = 90 b = 94.579 β = 90 c = 125.566 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 2016-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 2.24 47.29 95.4 0.091 15.3 7 30342
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 2.24 2.31 73.4 0.702 1.7 4.2
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 2.24 81.91 28729 1583 95.31 0.16299 0.16052 0.1693 0.20848 0.2073 RANDOM 44.27
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] 1.13 0.56 1.13 -3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.734 r_dihedral_angle_3_deg 17.773 r_dihedral_angle_4_deg 16.24 r_long_range_B_other 11.18 r_long_range_B_refined 11.147 r_scangle_other 8.448 r_mcangle_other 7.49 r_mcangle_it 7.471 r_dihedral_angle_1_deg 6.92 r_scbond_it 5.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.734 r_dihedral_angle_3_deg 17.773 r_dihedral_angle_4_deg 16.24 r_long_range_B_other 11.18 r_long_range_B_refined 11.147 r_scangle_other 8.448 r_mcangle_other 7.49 r_mcangle_it 7.471 r_dihedral_angle_1_deg 6.92 r_scbond_it 5.622 r_scbond_other 5.62 r_mcbond_it 4.807 r_mcbond_other 4.767 r_angle_refined_deg 2.306 r_angle_other_deg 1.231 r_chiral_restr 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2336 Nucleic Acid Atoms 321 Solvent Atoms 232 Heterogen Atoms 46
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement