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Crystal structure of the xNup93-Nb2t VHH antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ON5 prepared with Sculptor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 293.15 0.1 M CAPS (pH 10.5), 1.2 M sodium phosphate, 0.8 M potassium phosphate, 0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.43 64.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.968 α = 90 b = 99.968 β = 90 c = 30.707 γ = 120
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 2021-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.33 43.29 99.5 0.045 0.047 1 22.9 19.8 79377 20.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.33 1.41 1.818 1.919 0.715
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 1.41 32.72 1.38 34216 1674 99.95 0.1593 0.1579 0.1605 0.1882 0.1905 25.24
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 12.4346 f_angle_d 1.5347 f_chiral_restr 0.113 f_bond_d 0.0191 f_plane_restr 0.0096
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 898 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data scaling XDS data reduction