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DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.1 M Bicine, 0.1 M Tris base, 0.1 M Carboxylic acids, 10% PEG 20,000, 20% PEG 500 MME
Crystal Properties Matthews coefficient Solvent content 3.28 62.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.744 α = 90 b = 164.275 β = 90 c = 124.521 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 2016-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.25 37.05 99.26 0.121 12.25 7.1 27265
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 2.2335 2.254 1.619
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 2Y5G 2.25 37.05 25278 2000 99.22 0.22259 0.22014 0.2398 0.2533 0.2658 RANDOM 57.44
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] -0.77 0.42 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.421 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_3_deg 13.125 r_dihedral_angle_1_deg 6.471 r_long_range_B_refined 5.69 r_long_range_B_other 5.682 r_scangle_other 2.336 r_mcangle_it 1.996 r_mcangle_other 1.996 r_angle_refined_deg 1.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.421 r_dihedral_angle_4_deg 15.038 r_dihedral_angle_3_deg 13.125 r_dihedral_angle_1_deg 6.471 r_long_range_B_refined 5.69 r_long_range_B_other 5.682 r_scangle_other 2.336 r_mcangle_it 1.996 r_mcangle_other 1.996 r_angle_refined_deg 1.903 r_scbond_it 1.508 r_scbond_other 1.508 r_mcbond_other 1.253 r_mcbond_it 1.252 r_angle_other_deg 0.987 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 2206 Nucleic Acid Atoms 760 Solvent Atoms 93 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Coot model building DENZO data reduction HKL-3000 data scaling REFMAC phasing