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Principles for computational design of antibodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQ9 3QQ9, 2HFF experimental model PDB 2HFF 3QQ9, 2HFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M (NH4)2SO4
0.05M Tris pH=8.5
12.5% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.9 57.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.33 α = 90 b = 109.39 β = 90 c = 158.9 γ = 90
Symmetry Space Group P 21 21 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 RIGAKU RAXIS IV++ 2016-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-003 1.541
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3 90 93 0.195 3.8 4.2 21280
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 85.9 1.1 3.8
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 3QQ9, 2HFF 3 90 20906 1105 96.53 0.22521 0.22347 0.2275 0.25732 0.2603 RANDOM 51.253
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] -3.41 2.61 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.909 r_dihedral_angle_4_deg 19.225 r_dihedral_angle_3_deg 17.5 r_dihedral_angle_1_deg 7.872 r_long_range_B_refined 5.44 r_long_range_B_other 5.44 r_mcangle_it 2.391 r_mcangle_other 2.391 r_scangle_other 2.116 r_angle_refined_deg 1.376
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.909 r_dihedral_angle_4_deg 19.225 r_dihedral_angle_3_deg 17.5 r_dihedral_angle_1_deg 7.872 r_long_range_B_refined 5.44 r_long_range_B_other 5.44 r_mcangle_it 2.391 r_mcangle_other 2.391 r_scangle_other 2.116 r_angle_refined_deg 1.376 r_mcbond_it 1.344 r_mcbond_other 1.344 r_scbond_it 1.216 r_scbond_other 1.216 r_angle_other_deg 0.931 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6558 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALEPACK data scaling PHASER phasing