5FNV

a new complex structure of tubulin with an alpha-beta unsaturated lactone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I55PDB ENTRY 4I55

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.70.1M MES PH6.7;6% PEG4000 ;5% GLYCEROL;30MM CACL2;30MM MGCL2
Crystal Properties
Matthews coefficientSolvent content
3.1761

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.16α = 90
b = 157.2β = 90
c = 181.68γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U1SSRFBL19U1

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
12.6145.4994.80.0615.85.3880591.5
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)
12.612.6867.50.491.62.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4I552.61118.8883598439794.620.187730.185750.22555RANDOM79.794
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]
0.76-0.13-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.662
r_dihedral_angle_4_deg17.181
r_dihedral_angle_3_deg15.014
r_dihedral_angle_1_deg6.504
r_long_range_B_other5.695
r_long_range_B_refined5.693
r_scangle_other3.718
r_mcangle_other3.145
r_mcangle_it3.144
r_scbond_it2.536
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.662
r_dihedral_angle_4_deg17.181
r_dihedral_angle_3_deg15.014
r_dihedral_angle_1_deg6.504
r_long_range_B_other5.695
r_long_range_B_refined5.693
r_scangle_other3.718
r_mcangle_other3.145
r_mcangle_it3.144
r_scbond_it2.536
r_scbond_other2.488
r_mcbond_it2.033
r_mcbond_other2.029
r_angle_refined_deg1.636
r_angle_other_deg1.249
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.004
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
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16887
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms209

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing