9GNU | pdb_00009gnu

Tubulin in complex with a dioxane analog of zampanolide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293.150.1 M Mes / 0.1 M Imidazole pH 6.5, 0.03 M CaCl2 / 0.03 M MgCl2, 5 mM L-Tyrosine, 8 % glycerol, 5.5 % PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.856.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.197α = 90
b = 159.166β = 90
c = 178.367γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2020-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

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
12.248.1499.90.0810.0860.0270.99916.69.5151850
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)
12.22.2499.61.1630.3910.6991.99.6

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-VALUE2.248.139151759761099.8530.1660.16390.16450.20610.206852.554
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]
1.639-0.79-0.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.397
r_dihedral_angle_3_deg14.233
r_dihedral_angle_2_deg12.649
r_dihedral_angle_other_2_deg12.085
r_lrange_other9.441
r_lrange_it9.425
r_scangle_it7.744
r_scangle_other7.744
r_dihedral_angle_1_deg6.988
r_scbond_it5.397
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.397
r_dihedral_angle_3_deg14.233
r_dihedral_angle_2_deg12.649
r_dihedral_angle_other_2_deg12.085
r_lrange_other9.441
r_lrange_it9.425
r_scangle_it7.744
r_scangle_other7.744
r_dihedral_angle_1_deg6.988
r_scbond_it5.397
r_scbond_other5.397
r_mcangle_other4.411
r_mcangle_it4.41
r_mcbond_it3.281
r_mcbond_other3.281
r_angle_refined_deg2.344
r_angle_other_deg0.868
r_nbd_refined0.238
r_symmetry_xyhbond_nbd_refined0.208
r_xyhbond_nbd_refined0.196
r_symmetry_nbd_other0.195
r_nbtor_refined0.189
r_metal_ion_refined0.186
r_symmetry_nbd_refined0.179
r_nbd_other0.179
r_ncsr_local_group_10.135
r_ncsr_local_group_20.116
r_chiral_restr0.114
r_symmetry_nbtor_other0.087
r_symmetry_xyhbond_nbd_other0.06
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 Atoms17040
Nucleic Acid Atoms
Solvent Atoms880
Heterogen Atoms265

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing