X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Hanging Drop
pH 6.5
Temperature 277.0
Details MPD, pH 6.5, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 403.04 α = 90
b = 403.04 β = 90
c = 174.36 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-11-07
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C

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
3.6 35 99.2 0.085 -- -- 4.8 163468 163468 -3.0 -3.0 --
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)
3.6 3.73 99.2 0.923 -- -- 4.8 16146

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 3.6 34.644 -- 1.33 163397 163397 8155 99.21 -- 0.1594 0.1568 0.2066 FROM PDB ENTRY 2VQE
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 3.6 3.6413 -- 252 5075 0.2799 0.3241 -- 98.0
X Ray Diffraction 3.6413 3.6841 -- 296 5116 0.2627 0.2983 -- 100.0
X Ray Diffraction 3.6841 3.729 -- 280 5111 0.2535 0.3063 -- 99.0
X Ray Diffraction 3.729 3.7761 -- 302 5133 0.2359 0.2841 -- 100.0
X Ray Diffraction 3.7761 3.8258 -- 221 5130 0.2203 0.2778 -- 99.0
X Ray Diffraction 3.8258 3.8781 -- 275 5143 0.2101 0.2549 -- 99.0
X Ray Diffraction 3.8781 3.9334 -- 267 5153 0.2002 0.2489 -- 100.0
X Ray Diffraction 3.9334 3.9921 -- 270 5142 0.1928 0.2349 -- 99.0
X Ray Diffraction 3.9921 4.0543 -- 284 5125 0.1867 0.2376 -- 99.0
X Ray Diffraction 4.0543 4.1207 -- 305 5094 0.1703 0.2219 -- 100.0
X Ray Diffraction 4.1207 4.1916 -- 256 5174 0.1647 0.2303 -- 99.0
X Ray Diffraction 4.1916 4.2677 -- 242 5178 0.167 0.2574 -- 99.0
X Ray Diffraction 4.2677 4.3497 -- 309 5146 0.1564 0.205 -- 100.0
X Ray Diffraction 4.3497 4.4383 -- 264 5137 0.1496 0.1907 -- 100.0
X Ray Diffraction 4.4383 4.5346 -- 296 5107 0.1426 0.1911 -- 99.0
X Ray Diffraction 4.5346 4.6398 -- 258 5197 0.1366 0.1937 -- 99.0
X Ray Diffraction 4.6398 4.7556 -- 253 5180 0.1299 0.1928 -- 99.0
X Ray Diffraction 4.7556 4.8838 -- 259 5199 0.1289 0.2024 -- 99.0
X Ray Diffraction 4.8838 5.0271 -- 289 5151 0.1238 0.1721 -- 99.0
X Ray Diffraction 5.0271 5.1889 -- 252 5201 0.1197 0.1717 -- 100.0
X Ray Diffraction 5.1889 5.3737 -- 263 5216 0.1127 0.1716 -- 100.0
X Ray Diffraction 5.3737 5.588 -- 277 5188 0.1166 0.1698 -- 100.0
X Ray Diffraction 5.588 5.8411 -- 275 5208 0.1178 0.1855 -- 99.0
X Ray Diffraction 5.8411 6.1475 -- 246 5217 0.1223 0.179 -- 100.0
X Ray Diffraction 6.1475 6.5303 -- 263 5235 0.1302 0.1764 -- 99.0
X Ray Diffraction 6.5303 7.0306 -- 277 5242 0.1341 0.1898 -- 99.0
X Ray Diffraction 7.0306 7.731 -- 281 5240 0.1315 0.1936 -- 99.0
X Ray Diffraction 7.731 8.8334 -- 273 5296 0.1323 0.1768 -- 99.0
X Ray Diffraction 8.8334 11.0686 -- 281 5299 0.1484 0.1933 -- 99.0
X Ray Diffraction 11.0686 34.6456 -- 289 5209 0.2165 0.2362 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 167.854
Anisotropic B[1][1] -4.2438
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.2438
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.4876
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.484
f_plane_restr 0.009
f_chiral_restr 0.086
f_angle_d 1.495
f_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32507
Heterogen Atoms 256
Solvent Atoms 239

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: dev_978) Structure Solution
PHENIX (phenix.refine: dev_978) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection