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Crystal structure of a de novo-designed VHH targeting BHRF1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.2 M sodium acetate trihydrate, 0.1 M sodium citrate pH 5.5 and 8% (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.73 54.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.638 α = 90 b = 196.378 β = 90 c = 214.597 γ = 90
Symmetry Space Group P 2 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 2026-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.88560 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.4 47.9 99.9 0.995 8.2 8.4 50093
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.51 0.663
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 3.4 47.9 47514 2470 99.62 0.20677 0.20442 0.2104 0.25079 0.2581 RANDOM 135.651
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] 0.05 1.75 -1.8
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.869 r_long_range_B_other 23.869 r_scangle_other 17.279 r_mcangle_other 15.85 r_mcangle_it 15.849 r_dihedral_angle_3_deg 13.22 r_scbond_it 11.396 r_scbond_other 11.396 r_mcbond_it 10.385 r_mcbond_other 10.385
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.869 r_long_range_B_other 23.869 r_scangle_other 17.279 r_mcangle_other 15.85 r_mcangle_it 15.849 r_dihedral_angle_3_deg 13.22 r_scbond_it 11.396 r_scbond_other 11.396 r_mcbond_it 10.385 r_mcbond_other 10.385 r_dihedral_angle_2_deg 10.092 r_dihedral_angle_1_deg 6.97 r_angle_refined_deg 1.784 r_angle_other_deg 0.591 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 22139 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing