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 = 403.37 α = 90
b = 403.37 β = 90
c = 173.6 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
3.29 35 98.8 0.091 -- -- 4.8 210955 210955 -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)
3.294 3.42 99.9 0.875 -- -- 4.6 21141

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 3.294 34.924 -- 1.34 210877 210877 10630 98.6 -- 0.1698 0.1677 0.2103 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 3.294 3.3317 -- 360 6240 0.3065 0.3557 -- 93.0
X Ray Diffraction 3.3317 3.3708 -- 336 6677 0.279 0.308 -- 100.0
X Ray Diffraction 3.3708 3.4119 -- 384 6673 0.2769 0.3451 -- 100.0
X Ray Diffraction 3.4119 3.455 -- 360 6683 0.2621 0.291 -- 100.0
X Ray Diffraction 3.455 3.5005 -- 369 6626 0.2489 0.3024 -- 100.0
X Ray Diffraction 3.5005 3.5484 -- 361 6720 0.2394 0.2852 -- 100.0
X Ray Diffraction 3.5484 3.599 -- 376 6682 0.2252 0.2464 -- 100.0
X Ray Diffraction 3.599 3.6527 -- 355 6688 0.218 0.2487 -- 100.0
X Ray Diffraction 3.6527 3.7097 -- 373 6720 0.2096 0.2725 -- 100.0
X Ray Diffraction 3.7097 3.7704 -- 379 6704 0.1994 0.246 -- 100.0
X Ray Diffraction 3.7704 3.8354 -- 314 6735 0.1935 0.2558 -- 100.0
X Ray Diffraction 3.8354 3.905 -- 353 6705 0.1803 0.2053 -- 100.0
X Ray Diffraction 3.905 3.98 -- 345 6736 0.178 0.2238 -- 100.0
X Ray Diffraction 3.98 4.0612 -- 376 6708 0.1688 0.2186 -- 100.0
X Ray Diffraction 4.0612 4.1493 -- 376 6686 0.1627 0.204 -- 100.0
X Ray Diffraction 4.1493 4.2457 -- 330 6762 0.1546 0.2129 -- 100.0
X Ray Diffraction 4.2457 4.3517 -- 379 6695 0.1579 0.2099 -- 100.0
X Ray Diffraction 4.3517 4.4691 -- 367 6711 0.1542 0.2025 -- 100.0
X Ray Diffraction 4.4691 4.6003 -- 355 6720 0.1484 0.1982 -- 100.0
X Ray Diffraction 4.6003 4.7485 -- 324 6759 0.145 0.1849 -- 99.0
X Ray Diffraction 4.7485 4.9177 -- 347 6733 0.1398 0.1834 -- 99.0
X Ray Diffraction 4.9177 5.1141 -- 358 6744 0.1343 0.1817 -- 99.0
X Ray Diffraction 5.1141 5.346 -- 335 6724 0.1369 0.1815 -- 99.0
X Ray Diffraction 5.346 5.6268 -- 361 6708 0.1366 0.1966 -- 99.0
X Ray Diffraction 5.6268 5.9777 -- 333 6713 0.1429 0.1989 -- 98.0
X Ray Diffraction 5.9777 6.4366 -- 334 6723 0.1459 0.1813 -- 98.0
X Ray Diffraction 6.4366 7.0795 -- 349 6675 0.1398 0.1894 -- 97.0
X Ray Diffraction 7.0795 8.0927 -- 335 6682 0.141 0.1931 -- 97.0
X Ray Diffraction 8.0927 10.1543 -- 373 6678 0.1533 0.1848 -- 96.0
X Ray Diffraction 10.1543 34.9259 -- 333 6237 0.197 0.2135 -- 87.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 161.233
Anisotropic B[1][1] -13.3959
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -13.3959
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.1228
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.282
f_plane_restr 0.006
f_chiral_restr 0.07
f_angle_d 1.022
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32508
Heterogen Atoms 334
Solvent Atoms 407

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