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Structure of VHH-Fab complex with engineered Elbow FNQIKG, Crystal Kappa and SER substitutions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7RTH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 2% Tacsimate pH 5.0, 0.1 M Na citrate tribasic dihydrate, 16% PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.72 66.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.221 α = 90 b = 72.771 β = 90 c = 242.398 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 EIGER2 X 16M 2022-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.52 121.2 100 0.04 0.99 12.5 13.1 32276
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 2.52 2.62 100 0.78 0.37 0.8 13.6
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 MOLECULAR REPLACEMENT THROUGHOUT 2.52 121.2 30590 1595 99.91 0.1938 0.19126 0.1945 0.24291 0.2399 RANDOM 83.249
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] 1.81 -1.52 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.245 r_dihedral_angle_3_deg 18.942 r_dihedral_angle_4_deg 16.48 r_dihedral_angle_1_deg 7.437 r_long_range_B_refined 6.936 r_mcangle_it 3.59 r_scbond_it 2.561 r_mcbond_it 2.149 r_angle_refined_deg 1.118 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.245 r_dihedral_angle_3_deg 18.942 r_dihedral_angle_4_deg 16.48 r_dihedral_angle_1_deg 7.437 r_long_range_B_refined 6.936 r_mcangle_it 3.59 r_scbond_it 2.561 r_mcbond_it 2.149 r_angle_refined_deg 1.118 r_chiral_restr 0.09 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4319 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction