X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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 = 400.61 α = 90
b = 400.61 β = 90
c = 175.95 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
3.34 35 99.1 0.096 -- -- 3.2 202709 202709 -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)
3.342 3.47 99.9 0.802 -- -- 3.2 20193

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 3.3421 34.352 -- 1.33 202592 202592 10183 98.92 0.1737 0.1737 0.1719 0.2077 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 3.3421 3.3801 -- 312 6094 0.2911 0.3406 -- 95.0
X Ray Diffraction 3.3801 3.4198 -- 349 6426 0.2778 0.3082 -- 100.0
X Ray Diffraction 3.4198 3.4615 -- 359 6361 0.2772 0.2989 -- 100.0
X Ray Diffraction 3.4615 3.5052 -- 351 6403 0.2599 0.291 -- 100.0
X Ray Diffraction 3.5052 3.5513 -- 393 6371 0.2492 0.2877 -- 100.0
X Ray Diffraction 3.5513 3.5999 -- 327 6424 0.2366 0.2572 -- 100.0
X Ray Diffraction 3.5999 3.6513 -- 328 6423 0.222 0.2668 -- 100.0
X Ray Diffraction 3.6513 3.7057 -- 369 6382 0.2115 0.2258 -- 100.0
X Ray Diffraction 3.7057 3.7636 -- 350 6372 0.1963 0.2223 -- 100.0
X Ray Diffraction 3.7636 3.8252 -- 304 6496 0.1871 0.2219 -- 100.0
X Ray Diffraction 3.8252 3.8911 -- 341 6413 0.1793 0.2299 -- 100.0
X Ray Diffraction 3.8911 3.9617 -- 322 6434 0.1767 0.1928 -- 100.0
X Ray Diffraction 3.9617 4.0378 -- 365 6438 0.1731 0.2211 -- 100.0
X Ray Diffraction 4.0378 4.1201 -- 363 6394 0.1637 0.2055 -- 100.0
X Ray Diffraction 4.1201 4.2095 -- 322 6473 0.1554 0.1922 -- 100.0
X Ray Diffraction 4.2095 4.3073 -- 337 6453 0.1511 0.2011 -- 100.0
X Ray Diffraction 4.3073 4.4148 -- 367 6409 0.1458 0.1775 -- 100.0
X Ray Diffraction 4.4148 4.5339 -- 353 6427 0.1463 0.1775 -- 100.0
X Ray Diffraction 4.5339 4.667 -- 313 6478 0.1441 0.1949 -- 100.0
X Ray Diffraction 4.667 4.8172 -- 309 6465 0.1441 0.196 -- 100.0
X Ray Diffraction 4.8172 4.9889 -- 354 6430 0.1343 0.1822 -- 99.0
X Ray Diffraction 4.9889 5.188 -- 326 6482 0.1315 0.1564 -- 99.0
X Ray Diffraction 5.188 5.4232 -- 321 6462 0.1325 0.1827 -- 99.0
X Ray Diffraction 5.4232 5.7079 -- 351 6457 0.1335 0.1644 -- 99.0
X Ray Diffraction 5.7079 6.0637 -- 325 6482 0.1393 0.1831 -- 99.0
X Ray Diffraction 6.0637 6.529 -- 329 6459 0.1477 0.1957 -- 99.0
X Ray Diffraction 6.529 7.1806 -- 337 6421 0.1458 0.1847 -- 98.0
X Ray Diffraction 7.1806 8.2073 -- 323 6401 0.1513 0.1907 -- 97.0
X Ray Diffraction 8.2073 10.2939 -- 352 6412 0.1806 0.204 -- 96.0
X Ray Diffraction 10.2939 34.3537 -- 331 6267 0.217 0.234 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 114.001
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.137
f_plane_restr 0.004
f_chiral_restr 0.049
f_angle_d 0.816
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19153
Nucleic Acid Atoms 32522
Heterogen Atoms 196
Solvent Atoms 6

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: dev_1119) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction
DENZO data collection