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Crystal structure of single domain antibody kt75 of human Thyroglobulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4W6Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 4M K-acetate, 0.1 M sodium HEPES pH 7.0, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.751 α = 90 b = 47.589 β = 90 c = 64.237 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 CCD MAR CCD 165 mm 2022-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97777 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.35 38.75 100 0.055 0.059 0.021 0.999 18 7.9 26851 12.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 100 0.916 0.981 0.349 0.764 2.4 7.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.35 38.239 26796 1319 99.989 0.133 0.1304 0.1304 0.1744 0.1744 22.737
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] 0.881 -0.44 -0.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.852 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 10.769 r_rigid_bond_restr 9.416 r_dihedral_angle_1_deg 6.795 r_scangle_it 6.079 r_scangle_other 6.075 r_lrange_it 5.598 r_lrange_other 5.486 r_mcangle_it 5.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.852 r_dihedral_angle_4_deg 19.117 r_dihedral_angle_3_deg 10.769 r_rigid_bond_restr 9.416 r_dihedral_angle_1_deg 6.795 r_scangle_it 6.079 r_scangle_other 6.075 r_lrange_it 5.598 r_lrange_other 5.486 r_mcangle_it 5.175 r_scbond_it 5.148 r_scbond_other 5.143 r_mcangle_other 5.104 r_mcbond_it 4.907 r_mcbond_other 4.72 r_angle_refined_deg 1.621 r_angle_other_deg 0.577 r_symmetry_nbd_refined 0.431 r_nbd_refined 0.386 r_symmetry_xyhbond_nbd_refined 0.31 r_symmetry_nbd_other 0.204 r_nbd_other 0.202 r_nbtor_refined 0.2 r_xyhbond_nbd_refined 0.159 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 978 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing