☰ Navigation Tabs
Retrofitting antibodies with stabilizing mutations. Herceptin scFv mutant.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 3.5 M sodium formate, 100 mM sodium acetate (pH 4.5)
Crystal Properties Matthews coefficient Solvent content 2.74 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.19 α = 90 b = 91.19 β = 90 c = 114.35 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 315r 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 2.25 35.65 99.9 0.104 8.5 5 26621 40.6
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 2.25 2.37 100 0.86 1.8 4.9
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 2.25 35.65 25257 1329 99.82 0.2283 0.22618 0.2289 0.26906 0.2735 RANDOM 44.337
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] 0.63 0.32 0.63 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.619 r_dihedral_angle_4_deg 17.783 r_dihedral_angle_3_deg 16.11 r_dihedral_angle_1_deg 6.842 r_long_range_B_refined 4.271 r_long_range_B_other 4.271 r_mcangle_it 2.707 r_mcangle_other 2.706 r_scangle_other 2.653 r_scbond_it 1.718
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.619 r_dihedral_angle_4_deg 17.783 r_dihedral_angle_3_deg 16.11 r_dihedral_angle_1_deg 6.842 r_long_range_B_refined 4.271 r_long_range_B_other 4.271 r_mcangle_it 2.707 r_mcangle_other 2.706 r_scangle_other 2.653 r_scbond_it 1.718 r_scbond_other 1.717 r_mcbond_it 1.663 r_mcbond_other 1.663 r_angle_refined_deg 1.451 r_angle_other_deg 0.788 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 3137 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement