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Tubulin-colchicine-vinblastine: 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 7 291 PEG, PIPES BUFFER, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K. THE CRYSTAL OF TUBULIN-COLCHICINE:RB3-SLD COMPLEX WAS SOAKED WITH A 2 MILLI-MOLAR VINBLASTINE SOLUTION FOR 24 HOURS., pH 7.00
Crystal Properties Matthews coefficient Solvent content 3.81 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 324.852 α = 90 b = 324.852 β = 90 c = 54.208 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 2002-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 4.1 40 94.8 0.04 25 3.26 25286
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.1 4.2 76.6 0.33 2.5 2.25
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 (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 4.1 20 25034 23765 1269 95.39 0.21243 0.20943 0.2117 0.26886 0.2771 RANDOM 117.488
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] -0.77 -0.38 -0.77 1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.541 r_angle_refined_deg 1.906 r_symmetry_vdw_refined 0.344 r_nbd_refined 0.3 r_metal_ion_refined 0.279 r_xyhbond_nbd_refined 0.213 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 8.541 r_angle_refined_deg 1.906 r_symmetry_vdw_refined 0.344 r_nbd_refined 0.3 r_metal_ion_refined 0.279 r_xyhbond_nbd_refined 0.213 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13932 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 241
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement