X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 15 mg/ml of E2D2.(C85S)-Ub conjugate and an equimolar concentration of LubX (1-186), 0.2 M sodium tartrate, 0.1 M Tris-Cl (pH 8.5) and 25% PEG3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.29 α = 90
b = 119.29 β = 90
c = 49.81 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2013-12-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9789897 APS 19-ID

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
2.7 40 99.0 0.054 -- -- 5.0 -- 11243 -- -- --
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)
2.7 2.75 99.8 0.665 -- 4.07 5.0 --

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 2.7 35.855 -- 1.36 -- 10884 968 86.68 -- 0.1697 0.1668 0.2228 Random selection
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 2.7 2.8404 -- 87 1563 0.2443 0.366 -- 53.0
X Ray Diffraction 2.8404 3.0183 -- 128 2170 0.2306 0.2851 -- 74.0
X Ray Diffraction 3.0183 3.2512 -- 158 2699 0.2112 0.2829 -- 91.0
X Ray Diffraction 3.2512 3.5781 -- 159 2912 0.1831 0.23 -- 98.0
X Ray Diffraction 3.5781 4.0952 -- 152 2895 0.1467 0.1959 -- 98.0
X Ray Diffraction 4.0952 5.157 -- 141 2890 0.1283 0.1964 -- 97.0
X Ray Diffraction 5.157 35.8584 -- 143 2805 0.1569 0.1782 -- 95.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.005
f_plane_restr 0.007
f_angle_d 0.903
f_dihedral_angle_d 13.874
f_chiral_restr 0.044
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2653
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 53

Software

Software
Software Name Purpose
HKL-3000 data reduction
PHENIX phasing
PHENIX model building
Coot model building
PHENIX refinement version: (phenix.refine: 1.9_1692)
HKL-3000 data scaling