3E22

Tubulin-colchicine-soblidotin: Stathmin-like domain complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SA0PDB ENTRY 1SA0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291PEG, 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 coefficientSolvent content
3.7368

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 324.093α = 90
b = 324.093β = 90
c = 53.28γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSCmirrors2003-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9786ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.83598.30.063204.63273232732
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.83.8794.90.4692.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1SA03.8203217631414159897.630.23130.23130.2290.2948RANDOM95.446
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]
3.541.773.54-5.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.222
r_angle_refined_deg1.953
r_scangle_it0.548
r_symmetry_vdw_refined0.447
r_scbond_it0.339
r_nbd_refined0.296
r_mcangle_it0.252
r_metal_ion_refined0.236
r_xyhbond_nbd_refined0.212
r_mcbond_it0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.222
r_angle_refined_deg1.953
r_scangle_it0.548
r_symmetry_vdw_refined0.447
r_scbond_it0.339
r_nbd_refined0.296
r_mcangle_it0.252
r_metal_ion_refined0.236
r_xyhbond_nbd_refined0.212
r_mcbond_it0.139
r_chiral_restr0.133
r_symmetry_hbond_refined0.101
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13924
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms230

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling