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Crystal structure of the VHH and Trastuzumab-Fab complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N8Z experimental model PDB 5E7B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 20% (w/v) PEG 3350, 200mM Potassium nitrate
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.03 α = 90 b = 168.402 β = 90 c = 60.761 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC QUANTUM 270 2016-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 3 102.4 99.9 0.233 12.3 7.2 13760
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 1.103 0.762
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 FOURIER SYNTHESIS THROUGHOUT 3 102.4 13105 646 99.88 0.21357 0.21027 0.2174 0.279 0.2793 RANDOM 60.451
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] -5.23 -3.43 8.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.707 r_dihedral_angle_3_deg 18.386 r_dihedral_angle_4_deg 18.374 r_dihedral_angle_1_deg 8.552 r_long_range_B_refined 8.242 r_long_range_B_other 8.227 r_mcangle_it 5.34 r_mcangle_other 5.339 r_scangle_other 4.944 r_mcbond_it 3.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.707 r_dihedral_angle_3_deg 18.386 r_dihedral_angle_4_deg 18.374 r_dihedral_angle_1_deg 8.552 r_long_range_B_refined 8.242 r_long_range_B_other 8.227 r_mcangle_it 5.34 r_mcangle_other 5.339 r_scangle_other 4.944 r_mcbond_it 3.262 r_mcbond_other 3.262 r_scbond_it 2.947 r_scbond_other 2.944 r_angle_refined_deg 1.639 r_angle_other_deg 0.975 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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 4147 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing