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TBA G-quadruplex binding nanobody (free form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other nanobody with truncated cdr loops
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.25 298 1.6 M Ammonium sulphate
0.1 M HEPES, pH=7.25
cryoprotection=25% glycerol
Crystal Properties Matthews coefficient Solvent content 1.67 26.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.125 α = 90 b = 84.257 β = 90 c = 97.441 γ = 90
Symmetry Space Group C 2 2 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 EIGER X 16M 2021-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.53 48.721 99.8 0.068 0.074 0.029 0.999 16.1 6.5 15415
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 1.53 1.57 98.1 0.441 0.48 0.188 0.931 6.4
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 1.534 48.721 1.34 15380 1539 99.75 0.1732 0.1699 0.1752 0.2028 0.207
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 16.314 f_angle_d 0.941 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 914 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing