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Structure of HaCV P domain in complex with Nanobody 7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4X7E experimental model PDB 9DR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M Sodium fluoride, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 214.25 α = 90 b = 73.51 β = 94.11 c = 59.25 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 X 16M 2025-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX3 0.953720 Australian Synchrotron MX3
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 2.09 29.66 98.6 0.114 0.998 10.74 5.03 53856 32.62
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 2.09 2.14 96.9 0.754 0.843 0.371 0.667 1.9 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2.09 29.66 1.34 53776 2702 98.69 0.1837 0.1817 0.182 0.2225 0.2208 40
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 6.4796 f_angle_d 0.8862 f_chiral_restr 0.0572 f_bond_d 0.0077 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6441 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms
Software Software Software Name Purpose MxCuBE data collection PHENIX refinement XDS data reduction XDS data scaling PHASER phasing