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Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.01M Tri-sodium citrate, 16% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.38 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.595 α = 90 b = 140.394 β = 104.037 c = 61.961 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 EIGER X 9M 2019-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.953700 Australian Synchrotron MX1
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 2.46 70.197 99.9 0.177 3.6 7.7 28611
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.59 0.876 0.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2V8W 2.46 46.216 28587 1450 99.871 0.252 0.25 0.2526 0.2918 0.2922 34.813
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] 0.068 0.896 -2.743 1.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.797 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_4_deg 13.569 r_dihedral_angle_1_deg 6.66 r_lrange_it 3.227 r_lrange_other 3.186 r_mcangle_it 2.107 r_mcangle_other 2.107 r_scangle_it 1.665 r_scangle_other 1.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.797 r_dihedral_angle_3_deg 13.835 r_dihedral_angle_4_deg 13.569 r_dihedral_angle_1_deg 6.66 r_lrange_it 3.227 r_lrange_other 3.186 r_mcangle_it 2.107 r_mcangle_other 2.107 r_scangle_it 1.665 r_scangle_other 1.665 r_angle_refined_deg 1.185 r_mcbond_it 1.175 r_mcbond_other 1.175 r_angle_other_deg 1.076 r_scbond_it 0.933 r_scbond_other 0.933 r_symmetry_xyhbond_nbd_refined 0.225 r_symmetry_nbd_other 0.168 r_nbd_refined 0.162 r_nbtor_refined 0.152 r_xyhbond_nbd_refined 0.147 r_symmetry_nbd_refined 0.134 r_nbd_other 0.133 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.037 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4817 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing