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X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3G), which contains 1-beta-D-glucopyranosyl 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 = 94.798 α = 90 b = 94.798 β = 90 c = 125.326 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 1.73 125.33 94.4 1 19 20.1 41910
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 1.73 1.94 72 0.7 1.9 15.6
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 1.73 82.1 39863 2046 61.52 0.1795 0.178 0.1783 0.2072 0.2071 RANDOM 32.949
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] -0.06 -0.03 -0.06 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.724 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_4_deg 13.181 r_dihedral_angle_1_deg 7.396 r_angle_refined_deg 2.304 r_chiral_restr 0.157 r_bond_refined_d 0.016 r_gen_planes_refined 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2227 Nucleic Acid Atoms 312 Solvent Atoms 200 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