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Retrofitting antibodies with stabilizing mutations. Herceptin VL mutant F53D.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.1 M Sodium Malonate, 100 mM HEPES (pH 7.0), 1% (v/v) Jeffamine ED-2003
Crystal Properties Matthews coefficient Solvent content 3.2 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.58 α = 90 b = 103.75 β = 90 c = 110.21 γ = 90
Symmetry Space Group F 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
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 1.8 37.77 99.5 0.075 7.9 3.8 26083
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 1.8 1.9 99.9 0.428 2.4 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.8 37.77 24761 1322 99.21 0.1788 0.17701 0.1867 0.21264 0.222 RANDOM 24.19
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] 0.49 -0.65 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.493 r_dihedral_angle_4_deg 18.787 r_dihedral_angle_3_deg 11.709 r_dihedral_angle_1_deg 6.978 r_long_range_B_refined 5.196 r_long_range_B_other 5.16 r_scangle_other 3.744 r_scbond_it 2.552 r_scbond_other 2.551 r_mcangle_other 2.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.493 r_dihedral_angle_4_deg 18.787 r_dihedral_angle_3_deg 11.709 r_dihedral_angle_1_deg 6.978 r_long_range_B_refined 5.196 r_long_range_B_other 5.16 r_scangle_other 3.744 r_scbond_it 2.552 r_scbond_other 2.551 r_mcangle_other 2.295 r_mcangle_it 2.294 r_angle_refined_deg 1.984 r_mcbond_it 1.672 r_mcbond_other 1.637 r_angle_other_deg 0.914 r_chiral_restr 0.121 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1539 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement