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X-ray structure of the complex between human alpha thrombin and two duplex/quadruplex aptamers: NU172 and HD22_27mer
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 26% w/v PEG 3350, 0.2 M ammonium acetate and 0.1 M Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.87 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.927 α = 90 b = 77.616 β = 103.47 c = 95.408 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU SATURN 944 2018-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 3.1 60 99.8 1 6.6 3.7 22065
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 3.1 3.21 99.8 0.8 2.2 3.7
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 3.1 26.77 20946 1089 99.32 0.2027 0.1999 0.2073 0.257 0.2642 RANDOM 36.82
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] 2.73 -1.67 -4.28 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.393 r_dihedral_angle_3_deg 10.056 r_dihedral_angle_4_deg 8.919 r_dihedral_angle_1_deg 2.589 r_angle_other_deg 1.138 r_angle_refined_deg 1.067 r_chiral_restr 0.05 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.393 r_dihedral_angle_3_deg 10.056 r_dihedral_angle_4_deg 8.919 r_dihedral_angle_1_deg 2.589 r_angle_other_deg 1.138 r_angle_refined_deg 1.067 r_chiral_restr 0.05 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4462 Nucleic Acid Atoms 2214 Solvent Atoms 53 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing