X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

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

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 401.95 α = 90
b = 401.95 β = 90
c = 217.35 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 -- 2011-08-03
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 Monochromator 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
3.55 50 98.3 0.112 -- -- -- 209634 209634 -3.0 -3.0 120.364

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 3.55 50.0 -- 1.99 209597 209597 10476 98.33 -- 0.1535 0.151 0.201 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 3.5463 3.5866 -- 283 5955 0.282 0.3387 -- 89.0
X Ray Diffraction 3.5866 3.6288 -- 331 6679 0.2639 0.3245 -- 99.0
X Ray Diffraction 3.6288 3.673 -- 344 6560 0.2503 0.314 -- 99.0
X Ray Diffraction 3.673 3.7195 -- 349 6620 0.2434 0.3206 -- 99.0
X Ray Diffraction 3.7195 3.7684 -- 314 6614 0.2263 0.2858 -- 99.0
X Ray Diffraction 3.7684 3.82 -- 367 6639 0.2168 0.2782 -- 99.0
X Ray Diffraction 3.82 3.8746 -- 366 6598 0.2043 0.2608 -- 99.0
X Ray Diffraction 3.8746 3.9324 -- 373 6579 0.2037 0.2715 -- 99.0
X Ray Diffraction 3.9324 3.9938 -- 364 6575 0.2018 0.2696 -- 99.0
X Ray Diffraction 3.9938 4.0593 -- 366 6608 0.1911 0.2541 -- 99.0
X Ray Diffraction 4.0593 4.1292 -- 351 6581 0.1801 0.2279 -- 99.0
X Ray Diffraction 4.1292 4.2043 -- 362 6612 0.1747 0.2286 -- 99.0
X Ray Diffraction 4.2043 4.2851 -- 319 6680 0.1669 0.232 -- 99.0
X Ray Diffraction 4.2851 4.3725 -- 340 6613 0.1672 0.2239 -- 99.0
X Ray Diffraction 4.3725 4.4675 -- 366 6600 0.1628 0.2108 -- 99.0
X Ray Diffraction 4.4675 4.5714 -- 303 6693 0.1588 0.2188 -- 99.0
X Ray Diffraction 4.5714 4.6856 -- 340 6637 0.148 0.2065 -- 99.0
X Ray Diffraction 4.6856 4.8122 -- 366 6634 0.1413 0.1925 -- 99.0
X Ray Diffraction 4.8122 4.9537 -- 324 6662 0.1301 0.1831 -- 99.0
X Ray Diffraction 4.9537 5.1134 -- 337 6648 0.1302 0.1767 -- 99.0
X Ray Diffraction 5.1134 5.296 -- 373 6640 0.1223 0.1715 -- 99.0
X Ray Diffraction 5.296 5.5078 -- 363 6682 0.1215 0.1773 -- 99.0
X Ray Diffraction 5.5078 5.7581 -- 332 6683 0.1168 0.1803 -- 99.0
X Ray Diffraction 5.7581 6.0612 -- 329 6699 0.1115 0.1699 -- 99.0
X Ray Diffraction 6.0612 6.4402 -- 375 6711 0.1142 0.1743 -- 99.0
X Ray Diffraction 6.4402 6.9363 -- 366 6722 0.11 0.1686 -- 99.0
X Ray Diffraction 6.9363 7.6321 -- 341 6725 0.1064 0.1593 -- 99.0
X Ray Diffraction 7.6321 8.7315 -- 374 6751 0.112 0.1622 -- 98.0
X Ray Diffraction 8.7315 10.9816 -- 362 6812 0.1256 0.1697 -- 98.0
X Ray Diffraction 10.9816 50.0841 -- 396 6909 0.178 0.1968 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 142.922
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 21.212
f_plane_restr 0.012
f_chiral_restr 0.127
f_angle_d 2.778
f_bond_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19089
Nucleic Acid Atoms 32550
Heterogen Atoms 403
Solvent Atoms 1265

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: dev_1119) Structure Solution
PHENIX (phenix.refine: dev_1119) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction