5J2T

Tubulin-vinblastine complex


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details 6% PEG, 12% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.25 α = 90
b = 157.74 β = 90
c = 182.49 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-11-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.2 48.2 97.8 -- 0.158 -- 12.9 -- 150857 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.2 2.26 92.0 -- 3.461 0.71 11.4 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 2.2 48.168 -- 1.34 -- 150775 7494 97.79 -- 0.1959 0.1934 0.244 --
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.2 2.225 -- 207 4228 0.4054 0.457 -- 87.0
X Ray Diffraction 2.225 2.2512 -- 275 4551 0.3504 0.3541 -- 95.0
X Ray Diffraction 2.2512 2.2786 -- 242 4775 0.3519 0.3863 -- 99.0
X Ray Diffraction 2.2786 2.3075 -- 247 4830 0.3302 0.3621 -- 99.0
X Ray Diffraction 2.3075 2.3378 -- 264 4771 0.3104 0.3816 -- 99.0
X Ray Diffraction 2.3378 2.3699 -- 264 4766 0.294 0.3253 -- 99.0
X Ray Diffraction 2.3699 2.4037 -- 257 4782 0.29 0.3261 -- 99.0
X Ray Diffraction 2.4037 2.4396 -- 260 4800 0.2865 0.3313 -- 99.0
X Ray Diffraction 2.4396 2.4777 -- 239 4803 0.2754 0.3289 -- 99.0
X Ray Diffraction 2.4777 2.5183 -- 240 4801 0.2662 0.3221 -- 99.0
X Ray Diffraction 2.5183 2.5618 -- 225 4860 0.2508 0.3031 -- 99.0
X Ray Diffraction 2.5618 2.6083 -- 258 4785 0.2316 0.2914 -- 99.0
X Ray Diffraction 2.6083 2.6585 -- 254 4801 0.2315 0.2662 -- 99.0
X Ray Diffraction 2.6585 2.7128 -- 247 4857 0.2353 0.3267 -- 99.0
X Ray Diffraction 2.7128 2.7717 -- 234 4867 0.2376 0.2926 -- 99.0
X Ray Diffraction 2.7717 2.8362 -- 254 4618 0.247 0.3063 -- 96.0
X Ray Diffraction 2.8362 2.9071 -- 216 4476 0.23 0.3293 -- 92.0
X Ray Diffraction 2.9071 2.9857 -- 256 4841 0.217 0.2813 -- 99.0
X Ray Diffraction 2.9857 3.0736 -- 269 4799 0.1989 0.2601 -- 100.0
X Ray Diffraction 3.0736 3.1728 -- 262 4888 0.1894 0.243 -- 100.0
X Ray Diffraction 3.1728 3.2861 -- 245 4872 0.1966 0.2842 -- 100.0
X Ray Diffraction 3.2861 3.4177 -- 288 4801 0.1895 0.2702 -- 99.0
X Ray Diffraction 3.4177 3.5732 -- 246 4909 0.1762 0.217 -- 99.0
X Ray Diffraction 3.5732 3.7615 -- 238 4901 0.1686 0.2177 -- 99.0
X Ray Diffraction 3.7615 3.997 -- 249 4814 0.1619 0.196 -- 99.0
X Ray Diffraction 3.997 4.3055 -- 234 4516 0.1964 0.2408 -- 92.0
X Ray Diffraction 4.3055 4.7384 -- 251 4901 0.1352 0.1856 -- 99.0
X Ray Diffraction 4.7384 5.4233 -- 253 4936 0.1408 0.1931 -- 99.0
X Ray Diffraction 5.4233 6.8296 -- 265 4815 0.1769 0.2298 -- 97.0
X Ray Diffraction 6.8296 48.1794 -- 255 4917 0.1648 0.1875 -- 94.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_plane_restr 0.005
f_chiral_restr 0.042
f_dihedral_angle_d 16.213
f_angle_d 1.074
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17264
Nucleic Acid Atoms 0
Heterogen Atoms 195
Solvent Atoms 330

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
XDS data reduction
XSCALE data scaling
PHENIX phasing