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Crystal Structure of the Complex of the Recombinant Von Willebrand Factor AIM-A1 domain and VHH81 at 2.1 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 283 3.2 M ammonium sulphate, 0.08 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 3.32 62.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.234 α = 90 b = 65.234 β = 90 c = 233.231 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 283 PIXEL DECTRIS EIGER2 XE 16M 2020-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.117 62.9 92.4 0.048 1 15.1 5.2 19344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.117 2.3 69.2 0.645 0.6 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1AUQ 2.117 62.8 19344 921 92.4 0.198 0.1947 0.1947 0.2558 0.2556 51.291
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] -0.155 -0.155 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.913 r_lrange_other 24.864 r_lrange_it 24.822 r_dihedral_angle_4_deg 20.867 r_dihedral_angle_3_deg 16.499 r_scangle_it 7.914 r_scangle_other 7.88 r_dihedral_angle_1_deg 7.55 r_mcangle_it 5.937 r_mcangle_other 5.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.913 r_lrange_other 24.864 r_lrange_it 24.822 r_dihedral_angle_4_deg 20.867 r_dihedral_angle_3_deg 16.499 r_scangle_it 7.914 r_scangle_other 7.88 r_dihedral_angle_1_deg 7.55 r_mcangle_it 5.937 r_mcangle_other 5.935 r_scbond_it 5.244 r_scbond_other 5.211 r_mcbond_it 4.265 r_mcbond_other 4.265 r_angle_other_deg 2.339 r_angle_refined_deg 1.727 r_symmetry_nbd_refined 0.569 r_symmetry_xyhbond_nbd_refined 0.387 r_xyhbond_nbd_other 0.278 r_symmetry_nbd_other 0.22 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.162 r_nbd_other 0.154 r_symmetry_xyhbond_nbd_other 0.133 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.07 r_bond_other_d 0.035 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2620 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHENIX phasing