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X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3L), which contains 1-beta-D-lactopyranosyl residue in the side chain of Thy3 at N3.
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 7.5 293 200 mM KCl, 35% v/v pentaerythritol propoxylate, 50 mM HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.9 68.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.916 α = 90 b = 94.916 β = 90 c = 125.397 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 EIGER2 XE 16M 2019-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.58 82.2 95.9 1 23.2 19.6 54291
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 1.58 1.76 81.2 0.8 2 10.6
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 1.58 82.2 51616 2675 60.5 0.181 0.1797 0.1799 0.2057 0.2056 RANDOM 27.472
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.436 r_dihedral_angle_3_deg 14.749 r_dihedral_angle_4_deg 13.578 r_dihedral_angle_1_deg 7.303 r_angle_refined_deg 2.22 r_chiral_restr 0.153 r_bond_refined_d 0.015 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2239 Nucleic Acid Atoms 312 Solvent Atoms 202 Heterogen Atoms 32
Software Software Software Name Purpose autoPROC data processing STARANISO data processing PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling