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Crystal structure of scFv corresponding to human autoantibody b96.11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CBP experimental model PDB 5U68 experimental model PDB 5J74 experimental model PDB 5J75 experimental model PDB 5C6W experimental model PDB 5U0U experimental model PDB 4NIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 The hanging drop contained 1 microliter of mother liquor combined with 1 microliter of 20 mg/mL b96.11 scFv protein solution. Crystals formed as shards within 24 hours at 293 K, with final crystals being selected from well conditions containing 0.1M Bis-Tris pH 6.5, 2.5M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.544 α = 90 b = 103.963 β = 90 c = 85.088 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 PIXEL DECTRIS EIGER X 16M 2019-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.6 45.77 85.66 0.1372 0.968 3.92 1.9 26242 32.73
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 70.06 0.94 0.362 0.68 1.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.6 45.77 23377 1806 86.67 0.2329 0.2271 0.2234 0.3008 0.2969 34.1
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.009 f_angle_d 1.3159 f_chiral_restr 0.0728 f_bond_d 0.0095 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5343 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 20
Software Software Software Name Purpose Blu-Ice data collection PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing