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 = 402.04 α = 90
b = 402.04 β = 90
c = 176.39 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
3.28 35 99.1 0.093 -- -- 3.9 216436 216436 -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)
3.28 3.4 99.3 0.911 -- -- 4.0 21443

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 3.2811 34.475 -- 1.34 216354 216354 10916 99.06 0.1704 0.1704 0.1688 0.2012 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 3.2811 3.3183 -- 366 6623 0.2825 0.3113 -- 97.0
X Ray Diffraction 3.3183 3.3573 -- 372 6772 0.2663 0.2887 -- 99.0
X Ray Diffraction 3.3573 3.3983 -- 365 6800 0.2525 0.2817 -- 99.0
X Ray Diffraction 3.3983 3.4412 -- 350 6829 0.2455 0.2721 -- 100.0
X Ray Diffraction 3.4412 3.4865 -- 395 6754 0.241 0.2694 -- 99.0
X Ray Diffraction 3.4865 3.5342 -- 383 6770 0.2302 0.2661 -- 99.0
X Ray Diffraction 3.5342 3.5846 -- 379 6808 0.2186 0.2388 -- 100.0
X Ray Diffraction 3.5846 3.6381 -- 356 6807 0.1988 0.249 -- 99.0
X Ray Diffraction 3.6381 3.6949 -- 370 6818 0.1901 0.2066 -- 99.0
X Ray Diffraction 3.6949 3.7554 -- 384 6807 0.1785 0.2027 -- 99.0
X Ray Diffraction 3.7554 3.82 -- 346 6863 0.1738 0.2128 -- 100.0
X Ray Diffraction 3.82 3.8894 -- 337 6832 0.1586 0.196 -- 99.0
X Ray Diffraction 3.8894 3.9641 -- 356 6820 0.1582 0.2005 -- 99.0
X Ray Diffraction 3.9641 4.0449 -- 369 6816 0.1566 0.1837 -- 99.0
X Ray Diffraction 4.0449 4.1327 -- 400 6818 0.1487 0.1903 -- 99.0
X Ray Diffraction 4.1327 4.2287 -- 340 6869 0.1441 0.1754 -- 100.0
X Ray Diffraction 4.2287 4.3342 -- 356 6853 0.1454 0.1961 -- 100.0
X Ray Diffraction 4.3342 4.4512 -- 379 6850 0.1453 0.1863 -- 100.0
X Ray Diffraction 4.4512 4.5819 -- 386 6869 0.1436 0.1864 -- 100.0
X Ray Diffraction 4.5819 4.7294 -- 334 6897 0.1433 0.1868 -- 100.0
X Ray Diffraction 4.7294 4.898 -- 343 6943 0.1425 0.1826 -- 100.0
X Ray Diffraction 4.898 5.0935 -- 375 6873 0.1369 0.1895 -- 100.0
X Ray Diffraction 5.0935 5.3245 -- 338 6930 0.1391 0.1673 -- 100.0
X Ray Diffraction 5.3245 5.6041 -- 371 6899 0.1369 0.1884 -- 100.0
X Ray Diffraction 5.6041 5.9536 -- 353 6954 0.141 0.1669 -- 100.0
X Ray Diffraction 5.9536 6.4106 -- 345 6970 0.1545 0.1891 -- 100.0
X Ray Diffraction 6.4106 7.0507 -- 367 7017 0.1485 0.1855 -- 100.0
X Ray Diffraction 7.0507 8.0596 -- 356 6988 0.151 0.1777 -- 99.0
X Ray Diffraction 8.0596 10.1115 -- 383 6996 0.1727 0.1904 -- 99.0
X Ray Diffraction 10.1115 34.4767 -- 362 6593 0.2185 0.2313 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 117.537
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.836
f_plane_restr 0.004
f_chiral_restr 0.046
f_angle_d 0.771
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19153
Nucleic Acid Atoms 32504
Heterogen Atoms 184
Solvent Atoms 42

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