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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 sodium 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 5.05 75.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.33 α = 90 b = 120.69 β = 90 c = 208.94 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 PIXEL DECTRIS PILATUS3 2M 2017-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9677 ESRF MASSIF-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 2.8 104.51 99 0.074 0.086 0.042 0.988 12.4 4 21199
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 2.8 2.95 99.4 0.368 0.425 0.208 0.913 4.2
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 2.8 104.51 20089 1107 98.83 0.1611 0.1589 0.1683 0.203 0.2052 RANDOM 52.146
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] -4.24 -0.65 4.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.277 r_dihedral_angle_3_deg 10.885 r_dihedral_angle_4_deg 10.135 r_dihedral_angle_1_deg 3.369 r_angle_refined_deg 1.178 r_angle_other_deg 0.737 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.277 r_dihedral_angle_3_deg 10.885 r_dihedral_angle_4_deg 10.135 r_dihedral_angle_1_deg 3.369 r_angle_refined_deg 1.178 r_angle_other_deg 0.737 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2346 Nucleic Acid Atoms 543 Solvent Atoms 110 Heterogen Atoms 133
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction