9GMY | pdb_00009gmy

Tubulin in complex with an oxathiane analog of zampanolide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.7289.150.1 M Mes/0.1M Imidazole, 0.03M CaCl2/MgCl2, 5 mM L-Tyr, 2.5% glycerol, 4.6% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7855.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.907α = 90
b = 158.35β = 90
c = 178.836γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2024-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.9749.30699.90.0640.0670.0210.99918.89.420985038.629
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.97299.91.3860.5070.5391.48.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.9749.3062097371042799.930.1620.16020.16090.20240.20349.186
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]
0.7230.257-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.569
r_dihedral_angle_3_deg13.744
r_dihedral_angle_other_2_deg11.483
r_dihedral_angle_2_deg10.129
r_lrange_other9.102
r_lrange_it9.092
r_scangle_it7.103
r_scangle_other7.103
r_dihedral_angle_1_deg6.729
r_scbond_it5.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.569
r_dihedral_angle_3_deg13.744
r_dihedral_angle_other_2_deg11.483
r_dihedral_angle_2_deg10.129
r_lrange_other9.102
r_lrange_it9.092
r_scangle_it7.103
r_scangle_other7.103
r_dihedral_angle_1_deg6.729
r_scbond_it5.075
r_scbond_other5.075
r_mcangle_other3.987
r_mcangle_it3.985
r_mcbond_it3.181
r_mcbond_other3.181
r_angle_refined_deg2.298
r_dihedral_angle_other_3_deg1.62
r_angle_other_deg0.781
r_nbd_refined0.242
r_xyhbond_nbd_refined0.217
r_symmetry_nbd_refined0.204
r_symmetry_nbd_other0.193
r_nbtor_refined0.187
r_nbd_other0.186
r_symmetry_xyhbond_nbd_refined0.164
r_symmetry_xyhbond_nbd_other0.133
r_ncsr_local_group_10.133
r_chiral_restr_other0.132
r_metal_ion_refined0.124
r_ncsr_local_group_20.123
r_chiral_restr0.115
r_symmetry_nbtor_other0.086
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16991
Nucleic Acid Atoms
Solvent Atoms1294
Heterogen Atoms259

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing