4ZNY

Structure of the human TSG101-UEV Domain in complex with the PTAP motif of the p19 gag protein of the Human T-cell Leukemia type I virus


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 298.0
Details 30% PEG4k, 0.1 ammonium sulfate, 0.1 MES

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.62 α = 90
b = 119.74 β = 90
c = 41.64 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-06-28
Diffraction Radiation
Monochromator Protocol
Si(111) channel-cut crystal monochromator and a pair of KB mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97779 ESRF ID23-1

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
2.4 19.96 99.8 0.032 -- -- 4.7 -- 8020 -- -- 54.96
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)
2.4 2.49 100.0 0.279 -- 9.7 5.3 830

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
MOLECULAR REPLACEMENT 2.4 19.957 -- 2.0 -- 14340 750 96.59 -- 0.2306 0.2299 0.2431 --
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 2.4 2.585 -- 153 2568 0.3742 0.3851 -- 91.0
X Ray Diffraction 2.585 2.8444 -- 146 2663 0.37 0.4374 -- 95.0
X Ray Diffraction 2.8444 3.2545 -- 147 2750 0.3042 0.3582 -- 98.0
X Ray Diffraction 3.2545 4.0945 -- 143 2796 0.2266 0.2958 -- 99.0
X Ray Diffraction 4.0945 19.9578 -- 161 2813 0.1709 0.1488 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 76.975
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.03
f_angle_d 0.842
f_dihedral_angle_d 9.253
f_bond_d 0.003
f_plane_restr 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1158
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 5

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.8
PHASER phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
XDS data reduction