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De novo design and crystallographic validation of antibodies targeting a pre-selected epitope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IVK 3IVK, 1X2J experimental model PDB 1X2J 3IVK, 1X2J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 20% PEG3000, 200mM Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.08 40.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.499 α = 90 b = 69.808 β = 92.23 c = 99.562 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 2015-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91731 Diamond I04-1
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 1.85 30 99.1 0.049 11.2 3.1 85901
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 1.85 1.93 0.397
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 3IVK, 1X2J 1.85 29.69 77790 4108 99.16 0.22531 0.22316 0.2232 0.26531 0.2653 RANDOM 25.509
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] -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 12.915 r_dihedral_angle_1_deg 6.934 r_long_range_B_refined 6.033 r_mcangle_it 3.457 r_scbond_it 3.025 r_mcbond_it 2.472 r_angle_refined_deg 2.02 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 12.915 r_dihedral_angle_1_deg 6.934 r_long_range_B_refined 6.033 r_mcangle_it 3.457 r_scbond_it 3.025 r_mcbond_it 2.472 r_angle_refined_deg 2.02 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_refined 0.011 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 7769 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing