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 = 402.6 α = 90
b = 402.6 β = 90
c = 177.58 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 -- 2008-10-14
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
3.25 45 99.6 0.115 -- -- 3.7 226409 226409 -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)
3.249 3.37 100.0 0.811 -- -- 3.8 22444

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 3.249 44.389 -- 1.34 226222 226222 11411 99.61 -- 0.1731 0.1711 0.2109 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 3.249 3.2859 -- 394 7113 0.2983 0.3553 -- 100.0
X Ray Diffraction 3.2859 3.3246 -- 372 7088 0.2718 0.2833 -- 100.0
X Ray Diffraction 3.3246 3.3651 -- 398 7084 0.2573 0.2946 -- 100.0
X Ray Diffraction 3.3651 3.4077 -- 376 7167 0.2491 0.2899 -- 100.0
X Ray Diffraction 3.4077 3.4525 -- 380 7053 0.2418 0.2669 -- 100.0
X Ray Diffraction 3.4525 3.4998 -- 406 7117 0.2389 0.2795 -- 100.0
X Ray Diffraction 3.4998 3.5498 -- 393 7160 0.2169 0.2552 -- 100.0
X Ray Diffraction 3.5498 3.6027 -- 400 7067 0.2103 0.2602 -- 100.0
X Ray Diffraction 3.6027 3.659 -- 366 7122 0.2037 0.2435 -- 100.0
X Ray Diffraction 3.659 3.719 -- 405 7092 0.1941 0.2235 -- 100.0
X Ray Diffraction 3.719 3.783 -- 395 7144 0.1842 0.2351 -- 100.0
X Ray Diffraction 3.783 3.8518 -- 345 7174 0.1826 0.2175 -- 100.0
X Ray Diffraction 3.8518 3.9258 -- 380 7133 0.1763 0.2352 -- 100.0
X Ray Diffraction 3.9258 4.0059 -- 361 7162 0.1722 0.1973 -- 100.0
X Ray Diffraction 4.0059 4.093 -- 413 7109 0.1613 0.2061 -- 100.0
X Ray Diffraction 4.093 4.1881 -- 356 7188 0.1514 0.1828 -- 100.0
X Ray Diffraction 4.1881 4.2928 -- 379 7140 0.1476 0.1981 -- 100.0
X Ray Diffraction 4.2928 4.4087 -- 405 7142 0.1452 0.1846 -- 100.0
X Ray Diffraction 4.4087 4.5383 -- 397 7172 0.1437 0.1768 -- 100.0
X Ray Diffraction 4.5383 4.6847 -- 355 7204 0.1452 0.2028 -- 100.0
X Ray Diffraction 4.6847 4.8519 -- 344 7188 0.1412 0.1944 -- 100.0
X Ray Diffraction 4.8519 5.0459 -- 393 7160 0.1363 0.1813 -- 100.0
X Ray Diffraction 5.0459 5.2752 -- 362 7211 0.1381 0.1783 -- 100.0
X Ray Diffraction 5.2752 5.5528 -- 380 7210 0.1355 0.1861 -- 100.0
X Ray Diffraction 5.5528 5.9 -- 385 7235 0.135 0.1772 -- 100.0
X Ray Diffraction 5.9 6.3543 -- 347 7249 0.1394 0.1894 -- 100.0
X Ray Diffraction 6.3543 6.9916 -- 375 7231 0.1378 0.1849 -- 99.0
X Ray Diffraction 6.9916 7.9982 -- 368 7245 0.1401 0.1814 -- 99.0
X Ray Diffraction 7.9982 10.0575 -- 399 7217 0.1669 0.1977 -- 98.0
X Ray Diffraction 10.0575 44.393 -- 382 7234 0.2187 0.2323 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 98.2273
Anisotropic B[1][1] -8.6416
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -8.6416
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.2833
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 24.789
f_plane_restr 0.006
f_chiral_restr 0.068
f_angle_d 1.032
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19143
Nucleic Acid Atoms 32504
Heterogen Atoms 1037
Solvent Atoms 537

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