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Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BI7 1BI7, 3OGO experimental model PDB 3OGO 1BI7, 3OGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Molecular Dimensions Morpheus screen condition G4
Crystal Properties Matthews coefficient Solvent content 1.91 35.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.119 α = 90 b = 182.931 β = 90 c = 65.225 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 PILATUS3 6M 2018-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
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 1.74 91.47 100 0.101 0.119 0.061 0.998 9.2 6.8 26446
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 1.74 1.77 0.878 1.058 0.582 0.361 6.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BI7, 3OGO 1.74 91.465 26427 930 99.996 0.181 0.1798 0.1799 0.2086 0.2083 Random selection 27.959
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] 1.175 -1.038 -0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.079 r_dihedral_angle_4_deg 18.676 r_dihedral_angle_3_deg 15.269 r_lrange_it 6.946 r_lrange_other 6.927 r_dihedral_angle_1_deg 6.884 r_scangle_it 5.461 r_scangle_other 5.459 r_scbond_it 3.382 r_scbond_other 3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.079 r_dihedral_angle_4_deg 18.676 r_dihedral_angle_3_deg 15.269 r_lrange_it 6.946 r_lrange_other 6.927 r_dihedral_angle_1_deg 6.884 r_scangle_it 5.461 r_scangle_other 5.459 r_scbond_it 3.382 r_scbond_other 3.38 r_mcangle_other 3.186 r_mcangle_it 3.184 r_angle_refined_deg 2.081 r_mcbond_it 2.006 r_mcbond_other 1.979 r_angle_other_deg 1.41 r_nbd_other 0.249 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.194 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.16 r_symmetry_nbd_refined 0.158 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1854 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction PHASER phasing Coot model building