7L05

Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers, RB3 stathmin-like domain, and tubulin tyrosine ligase)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298PEG 3350, MES, CaCl2, MgCl2, glycerol
Crystal Properties
Matthews coefficientSolvent content
2.8757.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.088α = 90
b = 158.036β = 90
c = 181.014γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2016-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.000ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.25099.40.0770.0810.0233312.2150790-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2498.20.9320.9840.3110.7482.29.4

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 REPLACEMENTTHROUGHOUT4IHJ2.2145.62141073746697.750.18730.18570.2167RANDOM39.203
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]
0.58-0.37-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.725
r_dihedral_angle_4_deg16.574
r_dihedral_angle_3_deg14.342
r_dihedral_angle_1_deg6.663
r_angle_refined_deg1.543
r_angle_other_deg1.345
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.725
r_dihedral_angle_4_deg16.574
r_dihedral_angle_3_deg14.342
r_dihedral_angle_1_deg6.663
r_angle_refined_deg1.543
r_angle_other_deg1.345
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17281
Nucleic Acid Atoms
Solvent Atoms957
Heterogen Atoms236

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing