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Tubulin in complex with an oxathiane 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, HANGING DROP 6.7 289.15 0.1 M Mes/0.1M Imidazole, 0.03M CaCl2/MgCl2, 5 mM L-Tyr, 2.5% glycerol, 4.6% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.78 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.907 α = 90 b = 158.35 β = 90 c = 178.836 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 2024-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979 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 1.97 49.306 99.9 0.064 0.067 0.021 0.999 18.8 9.4 209850 38.629
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 1.97 2 99.9 1.386 0.507 0.539 1.4 8.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.97 49.306 209737 10427 99.93 0.162 0.1602 0.2024 0.1958 49.186
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] 0.723 0.257 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.569 r_dihedral_angle_3_deg 13.744 r_dihedral_angle_other_2_deg 11.483 r_dihedral_angle_2_deg 10.129 r_lrange_other 9.102 r_lrange_it 9.092 r_scangle_it 7.103 r_scangle_other 7.103 r_dihedral_angle_1_deg 6.729 r_scbond_it 5.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.569 r_dihedral_angle_3_deg 13.744 r_dihedral_angle_other_2_deg 11.483 r_dihedral_angle_2_deg 10.129 r_lrange_other 9.102 r_lrange_it 9.092 r_scangle_it 7.103 r_scangle_other 7.103 r_dihedral_angle_1_deg 6.729 r_scbond_it 5.075 r_scbond_other 5.075 r_mcangle_other 3.987 r_mcangle_it 3.985 r_mcbond_it 3.181 r_mcbond_other 3.181 r_angle_refined_deg 2.298 r_dihedral_angle_other_3_deg 1.62 r_angle_other_deg 0.781 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.217 r_symmetry_nbd_refined 0.204 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.187 r_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_other 0.133 r_ncsr_local_group_1 0.133 r_chiral_restr_other 0.132 r_metal_ion_refined 0.124 r_ncsr_local_group_2 0.123 r_chiral_restr 0.115 r_symmetry_nbtor_other 0.086 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 16991 Nucleic Acid Atoms Solvent Atoms 1294 Heterogen Atoms 259
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing