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Complex of anticoagulant RNA aptamer and human coagulation factor IXa (S195A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8EPH 8EPH, 3DD2 experimental model PDB 3DD2 8EPH, 3DD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 6_b4_cr4_1_1 VAPOR DIFFUSION, SITTING DROP 298 60 mM Na Citrate pH 5.0; 4% Tacsimate pH 7.0; 23% PEG 8000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.496 α = 90 b = 79.579 β = 101.78 c = 84.317 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 4 6_b4_cr4_1_1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2021-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 4 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97918 APS 24-ID-C
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 4 2.65 60.24 98.5 0.108 0.128 0.068 0.997 8.2 3.5 27106
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) 4 2.65 2.77 96.4 2.29 2.687 1.395 0.384 3.6
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 8EPH, 3DD2 2.65 60.24 25317 1313 96.58 0.2328 0.2313 0.2607 0.2416 RANDOM 93.716
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] 0.79 -0.05 -2.16 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.266 r_dihedral_angle_3_deg 15.156 r_dihedral_angle_4_deg 10.536 r_dihedral_angle_1_deg 6.074 r_angle_refined_deg 1.759 r_angle_other_deg 1.183 r_chiral_restr 0.111 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.266 r_dihedral_angle_3_deg 15.156 r_dihedral_angle_4_deg 10.536 r_dihedral_angle_1_deg 6.074 r_angle_refined_deg 1.759 r_angle_other_deg 1.183 r_chiral_restr 0.111 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4512 Nucleic Acid Atoms 1344 Solvent Atoms 10 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction