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Tubulin in complex with a dioxane analog of zampanolide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.1 M Mes / 0.1 M Imidazole pH 6.5, 0.03 M CaCl2 / 0.03 M MgCl2, 5 mM L-Tyrosine, 8 % glycerol, 5.5 % PEG4000
Crystal Properties Matthews coefficient Solvent content 2.8 56.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.197 α = 90 b = 159.166 β = 90 c = 178.367 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M 2020-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
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 2.2 48.14 99.9 0.081 0.086 0.027 0.999 16.6 9.5 151850
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 99.6 1.163 0.391 0.699 1.9 9.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.2 48.139 151759 7610 99.853 0.166 0.1639 0.1645 0.2061 0.2068 52.554
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] 1.639 -0.79 -0.849
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.397 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_2_deg 12.649 r_dihedral_angle_other_2_deg 12.085 r_lrange_other 9.441 r_lrange_it 9.425 r_scangle_it 7.744 r_scangle_other 7.744 r_dihedral_angle_1_deg 6.988 r_scbond_it 5.397
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.397 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_2_deg 12.649 r_dihedral_angle_other_2_deg 12.085 r_lrange_other 9.441 r_lrange_it 9.425 r_scangle_it 7.744 r_scangle_other 7.744 r_dihedral_angle_1_deg 6.988 r_scbond_it 5.397 r_scbond_other 5.397 r_mcangle_other 4.411 r_mcangle_it 4.41 r_mcbond_it 3.281 r_mcbond_other 3.281 r_angle_refined_deg 2.344 r_angle_other_deg 0.868 r_nbd_refined 0.238 r_symmetry_xyhbond_nbd_refined 0.208 r_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.189 r_metal_ion_refined 0.186 r_symmetry_nbd_refined 0.179 r_nbd_other 0.179 r_ncsr_local_group_1 0.135 r_ncsr_local_group_2 0.116 r_chiral_restr 0.114 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.06 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17040 Nucleic Acid Atoms Solvent Atoms 880 Heterogen Atoms 265
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing