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X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of potassium ions.
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 7 293 Tacsimate 50 % v/v, pH 7.0
Crystal Properties Matthews coefficient Solvent content 4.81 74.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.875 α = 90 b = 113.595 β = 90 c = 208.034 γ = 90
Symmetry Space Group I 2 2 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 CCD RIGAKU SATURN 944 2016-01-08 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) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.5 50 93.8 0.079 0.087 0.036 14.7 5.3 26684
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 2.5 2.59 64.7 0.317 0.371 0.187 0.859 3.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1PPB 2.5 104.02 25367 1312 93.74 0.1708 0.1691 0.2054 0.2107 RANDOM 48.197
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] -3.8 -2.99 6.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.335 r_dihedral_angle_4_deg 15.243 r_dihedral_angle_3_deg 11.171 r_dihedral_angle_1_deg 2.748 r_angle_refined_deg 1.482 r_angle_other_deg 0.846 r_chiral_restr 0.18 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.335 r_dihedral_angle_4_deg 15.243 r_dihedral_angle_3_deg 11.171 r_dihedral_angle_1_deg 2.748 r_angle_refined_deg 1.482 r_angle_other_deg 0.846 r_chiral_restr 0.18 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2356 Nucleic Acid Atoms 543 Solvent Atoms 129 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing