5BMV

CRYSTAL STRUCTURE OF TUBULIN-STATHMIN-TTL-Vinblastine COMPLEX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4TV8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2936% PEG, 5% glycerol, 0.1M MES, 30 mM CaCl2, 30 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.9358.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.47α = 90
b = 157.42β = 90
c = 183.18γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-01-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97853SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.550100196.7106106

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4TV82.55094797490699.50.1870.1840.235RANDOM53.32
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]
0.02-0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.698
r_dihedral_angle_3_deg17.825
r_dihedral_angle_4_deg16.449
r_dihedral_angle_1_deg6.889
r_mcangle_it5.954
r_mcbond_it3.931
r_mcbond_other3.929
r_angle_refined_deg1.727
r_angle_other_deg0.867
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.698
r_dihedral_angle_3_deg17.825
r_dihedral_angle_4_deg16.449
r_dihedral_angle_1_deg6.889
r_mcangle_it5.954
r_mcbond_it3.931
r_mcbond_other3.929
r_angle_refined_deg1.727
r_angle_other_deg0.867
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.003
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
MAIN-CHAIN ANGLE OTHER ATOMS (A**2)
r_scbond_it
SIDE-CHAIN BOND OTHER ATOMS (A**2)
r_scangle_it
SIDE-CHAIN ANGLE OTHER ATOMS (A**2)
LONG RANGE B REFINED ATOMS (A**2)
LONG RANGE B OTHER ATOMS (A**2)
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17401
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms283

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction