X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details 5% isopropanol, optimised mixture of salts, 50mM Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 122.41 α = 90
b = 122.41 β = 90
c = 178.29 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-08-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 DIAMOND I03

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
2.9 50 98.1 0.074 0.074 -- 5.6 -- 64923 0.0 -3.0 80.77
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)
2.9 3.0 -- 0.422 0.422 2.19 5.8 --

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 2.9 26.731 -- 1.96 -- 64564 6484 97.64 -- 0.1867 0.1831 0.2182 random
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 2.9004 2.9333 -- 221 1915 0.2548 0.2933 -- 98.0
X Ray Diffraction 2.9333 2.9678 -- 222 1968 0.2428 0.2851 -- 99.0
X Ray Diffraction 2.9678 3.0039 -- 219 1962 0.2259 0.261 -- 99.0
X Ray Diffraction 3.0039 3.0419 -- 211 1937 0.237 0.2732 -- 98.0
X Ray Diffraction 3.0419 3.0819 -- 236 2006 0.2246 0.284 -- 99.0
X Ray Diffraction 3.0819 3.124 -- 225 1943 0.2183 0.2664 -- 99.0
X Ray Diffraction 3.124 3.1686 -- 196 1947 0.2372 0.2547 -- 99.0
X Ray Diffraction 3.1686 3.2158 -- 212 2056 0.2485 0.3158 -- 99.0
X Ray Diffraction 3.2158 3.266 -- 220 1874 0.2513 0.306 -- 99.0
X Ray Diffraction 3.266 3.3194 -- 208 2018 0.232 0.2841 -- 99.0
X Ray Diffraction 3.3194 3.3766 -- 210 1984 0.2279 0.2723 -- 100.0
X Ray Diffraction 3.3766 3.4378 -- 219 1946 0.2227 0.2591 -- 100.0
X Ray Diffraction 3.4378 3.5038 -- 206 2002 0.2075 0.2464 -- 100.0
X Ray Diffraction 3.5038 3.5752 -- 203 1968 0.1954 0.2394 -- 99.0
X Ray Diffraction 3.5752 3.6527 -- 212 2007 0.1933 0.2359 -- 100.0
X Ray Diffraction 3.6527 3.7375 -- 211 2019 0.1745 0.2103 -- 100.0
X Ray Diffraction 3.7375 3.8307 -- 237 1921 0.1645 0.1895 -- 100.0
X Ray Diffraction 3.8307 3.9339 -- 245 2017 0.1541 0.1952 -- 100.0
X Ray Diffraction 3.9339 4.0493 -- 219 1910 0.1505 0.1769 -- 99.0
X Ray Diffraction 4.0493 4.1796 -- 209 1980 0.1525 0.1806 -- 100.0
X Ray Diffraction 4.1796 4.3283 -- 250 2006 0.1453 0.1779 -- 100.0
X Ray Diffraction 4.3283 4.5009 -- 223 1950 0.1326 0.1639 -- 100.0
X Ray Diffraction 4.5009 4.7047 -- 241 1978 0.1251 0.1599 -- 100.0
X Ray Diffraction 4.7047 4.9512 -- 230 1936 0.1344 0.1719 -- 100.0
X Ray Diffraction 4.9512 5.2592 -- 215 1981 0.1503 0.1711 -- 100.0
X Ray Diffraction 5.2592 5.6617 -- 229 1983 0.1535 0.179 -- 100.0
X Ray Diffraction 5.6617 6.225 -- 228 1968 0.175 0.2101 -- 100.0
X Ray Diffraction 6.225 7.1109 -- 215 2012 0.1668 0.2101 -- 100.0
X Ray Diffraction 7.1109 8.9036 -- 209 1886 0.1617 0.1941 -- 95.0
X Ray Diffraction 8.9036 26.7318 -- 103 1000 0.2171 0.2575 -- 50.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic+TLS
Mean Isotropic B 88.666
Anisotropic B[1][1] -2.415
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.415
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.829
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.095
f_dihedral_angle_d 19.692
f_angle_d 1.403
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10721
Nucleic Acid Atoms 730
Heterogen Atoms 54
Solvent Atoms 14

Software

Computing
Computing Package Purpose
GDA Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
phaser Structure Solution
PHENIX (phenix.refine) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine) refinement
phaser model building
GDA data collection