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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 delta
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 PEG 3350 30% w/v, 0.2 M sodium malonate, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.62 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.87 α = 90 b = 75.87 β = 90 c = 146.9 γ = 120
Symmetry Space Group P 32 2 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 2021-02-10 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 2.5 49.02 100 1 39.7 18.8 17665
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 2.5 2.54 100 0.8 2.5
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 2.5 49.02 16714 951 99.95 0.2485 0.2459 0.246 0.2954 0.2955 RANDOM 77.887
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] 0.03 0.02 0.03 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.168 r_dihedral_angle_3_deg 18.123 r_dihedral_angle_4_deg 15.279 r_dihedral_angle_1_deg 7.367 r_angle_refined_deg 1.102 r_chiral_restr 0.094 r_gen_planes_refined 0.005 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2240 Nucleic Acid Atoms 435 Solvent Atoms 15 Heterogen Atoms 130
Software Software Software Name Purpose autoPROC data processing PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling XDS data reduction