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Crystal structure of Fab fragment of bevacizumab bound to DNA aptamer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BJ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 Sulfate
Crystal Properties Matthews coefficient Solvent content 2.18 43.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.543 α = 90 b = 130.599 β = 103.59 c = 90.244 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 EIGER X 16M 2018-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.7 20 99.3 0.048 12.6 3.4 104111
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 1.7 1.79 0.511
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 1bj1 1.7 19.71 99026 5050 99.27 0.17952 0.178 0.1798 0.21002 0.2114 RANDOM 31.467
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.034 r_dihedral_angle_4_deg 17.313 r_dihedral_angle_3_deg 13.354 r_dihedral_angle_1_deg 6.864 r_long_range_B_refined 4.894 r_mcangle_it 2.077 r_scbond_it 1.664 r_mcbond_it 1.272 r_angle_refined_deg 1.104 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.034 r_dihedral_angle_4_deg 17.313 r_dihedral_angle_3_deg 13.354 r_dihedral_angle_1_deg 6.864 r_long_range_B_refined 4.894 r_mcangle_it 2.077 r_scbond_it 1.664 r_mcbond_it 1.272 r_angle_refined_deg 1.104 r_chiral_restr 0.079 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6610 Nucleic Acid Atoms 990 Solvent Atoms 651 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing