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Complex of human thrombin (S195A) bound to a bivalent inhibitor comprised of DNA Aptamer HD22 conjugated to Dabigatran with a linker.
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, SITTING DROP 6 298 0.1 M MES monohydrate pH 6, 22% (v/v) polyethylene glycol 400 (Hampton PEGRx1 #08)
Crystal Properties Matthews coefficient Solvent content 3.43 64.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.626 α = 90 b = 81.626 β = 90 c = 190.514 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 9M 2022-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.979354 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 41.2 100 0.153 0.159 0.042 0.99 8.9 14.4 33265
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 5.99 100 5.615 5.808 1.473 0.4 15.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.207 41.138 33010 1999 99.23 0.216 0.2138 0.2203 0.2446 0.2474 RANDOM 80.055
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] -0.805 -0.805 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.259 r_dihedral_angle_3_deg 13.161 r_lrange_other 11.889 r_lrange_it 11.886 r_scangle_it 7.576 r_scangle_other 7.575 r_dihedral_angle_1_deg 6.705 r_scbond_it 4.994 r_scbond_other 4.993 r_dihedral_angle_2_deg 4.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.259 r_dihedral_angle_3_deg 13.161 r_lrange_other 11.889 r_lrange_it 11.886 r_scangle_it 7.576 r_scangle_other 7.575 r_dihedral_angle_1_deg 6.705 r_scbond_it 4.994 r_scbond_other 4.993 r_dihedral_angle_2_deg 4.746 r_mcangle_it 4.39 r_mcangle_other 4.39 r_mcbond_it 3.03 r_mcbond_other 3.028 r_angle_refined_deg 1.066 r_dihedral_angle_other_2_deg 0.585 r_angle_other_deg 0.347 r_xyhbond_nbd_refined 0.256 r_symmetry_nbd_other 0.194 r_nbd_refined 0.193 r_nbtor_refined 0.193 r_nbd_other 0.178 r_symmetry_nbd_refined 0.107 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.047 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_symmetry_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2371 Nucleic Acid Atoms 629 Solvent Atoms 14 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement autoPROC data scaling XDS data reduction PHASER phasing