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Tubulin-colchicine-phomopsin A: 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 0.7mM Phomopsin A solution for 24 hours., pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.82 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 327.126 α = 90 b = 327.126 β = 90 c = 53.672 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 2003-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.976 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 4.1 40 96 0.078 12.2 2.6 26640 25575
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 4.1 4.2 90.8 0.428 1.9
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 4.1 20 26330 25389 1277 96.43 0.21781 0.21781 0.21521 0.2165 0.26471 0.2713 RANDOM 95.778
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] 3.55 1.77 3.55 -5.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.774 r_angle_refined_deg 2.041 r_metal_ion_refined 0.574 r_symmetry_hbond_refined 0.449 r_symmetry_vdw_refined 0.385 r_nbd_refined 0.305 r_xyhbond_nbd_refined 0.241 r_chiral_restr 0.131 r_bond_refined_d 0.017 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.774 r_angle_refined_deg 2.041 r_metal_ion_refined 0.574 r_symmetry_hbond_refined 0.449 r_symmetry_vdw_refined 0.385 r_nbd_refined 0.305 r_xyhbond_nbd_refined 0.241 r_chiral_restr 0.131 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_mcbond_it r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13966 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 292
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling