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X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form gamma
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 3350 25% w/v, ammonium acetate 0.2 M, Bis-Tris 0.1 M, pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.28 65.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.62 α = 90 b = 114.86 β = 117.25 c = 83.44 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 PIXEL DECTRIS PILATUS 6M 2021-02-05 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 3.03 68.13 99.6 1 11.2 6.6 24860
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 3.03 3.09 99.8 0.8 2.2
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 3.03 68.13 23638 1223 99.58 0.2027 0.2006 0.2006 0.2429 0.2435 RANDOM 68.215
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] -0.41 0.03 0.27 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.884 r_dihedral_angle_4_deg 17.353 r_dihedral_angle_3_deg 17.301 r_dihedral_angle_1_deg 6.909 r_angle_refined_deg 1.031 r_chiral_restr 0.099 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4488 Nucleic Acid Atoms 1057 Solvent Atoms 29 Heterogen Atoms 526
Software Software Software Name Purpose autoPROC data processing PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling