X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_angle_d 2.778
f_bond_d 0.02
f_plane_restr 0.012
f_dihedral_angle_d 21.212
f_chiral_restr 0.127
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

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement version: dev_1119
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
PHENIX phasing version: dev_1119