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Tubulin-colchicine-soblidotin: Stathmin-like domain complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SA0 PDB ENTRY 1SA0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 PEG, PIPES buffer, The crystal of tubulin-colchicine:RB3-SLD complex was soaked with a 2.0mM soblidotin solution for 24 hours., pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.73 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 324.093 α = 90 b = 324.093 β = 90 c = 53.28 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 CCD ADSC mirrors 2003-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9786 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 3.8 35 98.3 0.063 20 4.6 32732 32732
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.8 3.87 94.9 0.469 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SA0 3.8 20 32176 31414 1598 97.63 0.2313 0.2313 0.229 0.2398 0.2948 0.2939 RANDOM 95.446
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] 3.54 1.77 3.54 -5.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.222 r_angle_refined_deg 1.953 r_scangle_it 0.548 r_symmetry_vdw_refined 0.447 r_scbond_it 0.339 r_nbd_refined 0.296 r_mcangle_it 0.252 r_metal_ion_refined 0.236 r_xyhbond_nbd_refined 0.212 r_mcbond_it 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.222 r_angle_refined_deg 1.953 r_scangle_it 0.548 r_symmetry_vdw_refined 0.447 r_scbond_it 0.339 r_nbd_refined 0.296 r_mcangle_it 0.252 r_metal_ion_refined 0.236 r_xyhbond_nbd_refined 0.212 r_mcbond_it 0.139 r_chiral_restr 0.133 r_symmetry_hbond_refined 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13924 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 230
Software Software Software Name Purpose AMoRE phasing REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling