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X-ray structure of the complex between human alpha thrombin and a duplex/quadruplex 31-mer DNA aptamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.2 M sodium malonate pH 7, 18 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.319 α = 90 b = 124.42 β = 90 c = 40.44 γ = 90
Symmetry Space Group P 21 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 CCD RIGAKU SATURN 944 2014-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.98 70 90.1 0.134 7.3 3.2 7828
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.98 3.11 85.5 0.558 2.3 2.9
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 4DII 2.98 65.67 7406 411 92.6 0.169 0.166 0.196 0.231 0.2059 RANDOM 54.54
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] 0.84 -0.8 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_3_deg 18.414 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_1_deg 7.469 r_long_range_B_refined 7.125 r_long_range_B_other 7.089 r_scangle_other 4.598 r_mcangle_it 4.005 r_mcangle_other 4.003 r_scbond_it 2.838
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.004 r_dihedral_angle_3_deg 18.414 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_1_deg 7.469 r_long_range_B_refined 7.125 r_long_range_B_other 7.089 r_scangle_other 4.598 r_mcangle_it 4.005 r_mcangle_other 4.003 r_scbond_it 2.838 r_scbond_other 2.822 r_mcbond_it 2.452 r_mcbond_other 2.451 r_angle_refined_deg 1.719 r_angle_other_deg 1.2 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2245 Nucleic Acid Atoms 612 Solvent Atoms 70 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing