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X-ray structure of the complex between human alpha thrombin and the duplex/quadruplex aptamer M08s-1_41mer
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 6.5 293 PEG 8000 20% w/v, magnesium acetate 0.2 M, sodium cacodylate 0.1 M, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.96 61.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.06 α = 90 b = 75.49 β = 90 c = 114.31 γ = 90
Symmetry Space Group P 21 2 21
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 2021-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0000 ELETTRA 11.2C
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 2.8 50 100 1 10.1 37.5 15101
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 2.8 3 100 0.7 1.5
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 (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 2.8 46.27 14350 721 99.97 0.20849 0.20627 0.2066 0.2517 0.2519 RANDOM 77.137
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] -0.29 0.51 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.795 r_long_range_B_refined 9.711 r_dihedral_angle_1_deg 6.666 r_dihedral_angle_2_deg 4.953 r_mcangle_it 4.479 r_scbond_it 4.024 r_mcbond_it 2.702 r_angle_refined_deg 1.28 r_chiral_restr 0.113 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.795 r_long_range_B_refined 9.711 r_dihedral_angle_1_deg 6.666 r_dihedral_angle_2_deg 4.953 r_mcangle_it 4.479 r_scbond_it 4.024 r_mcbond_it 2.702 r_angle_refined_deg 1.28 r_chiral_restr 0.113 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2342 Nucleic Acid Atoms 846 Solvent Atoms 21 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing autoPROC data processing