1Z2B

Tubulin-colchicine-vinblastine: 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
17291PEG, 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 coefficientSolvent content
3.8168

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 324.852α = 90
b = 324.852β = 90
c = 54.208γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2002-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
14.14094.80.04253.2625286
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
14.14.276.60.332.52.25

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1SA04.1202503423765126995.390.212430.209430.26886RANDOM117.488
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]
-0.77-0.38-0.771.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.541
r_angle_refined_deg1.906
r_symmetry_vdw_refined0.344
r_nbd_refined0.3
r_metal_ion_refined0.279
r_xyhbond_nbd_refined0.213
r_symmetry_hbond_refined0.131
r_chiral_restr0.12
r_bond_refined_d0.017
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg8.541
r_angle_refined_deg1.906
r_symmetry_vdw_refined0.344
r_nbd_refined0.3
r_metal_ion_refined0.279
r_xyhbond_nbd_refined0.213
r_symmetry_hbond_refined0.131
r_chiral_restr0.12
r_bond_refined_d0.017
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms13932
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms241

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement