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 = 397.81 α = 90
b = 397.81 β = 90
c = 214.91 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
PIXEL DECTRIS PILATUS 6M -- 2011-02-06
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.98 SLS X06SA

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
3.5 50 99.6 0.12 -- -- -- 214567 214567 -3.0 -3.0 109.741
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)
3.5 3.71 97.6 0.988 -- 2.01 -- --

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
MOLECULAR REPLACEMENT 3.5 49.841 -- 1.99 214519 214519 10714 99.59 -- 0.1604 0.1582 0.2011 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 3.4965 3.5362 -- 313 6208 0.2974 0.3552 -- 91.0
X Ray Diffraction 3.5362 3.5778 -- 324 6661 0.2737 0.3249 -- 98.0
X Ray Diffraction 3.5778 3.6215 -- 335 6663 0.245 0.2926 -- 99.0
X Ray Diffraction 3.6215 3.6673 -- 344 6756 0.2319 0.2911 -- 100.0
X Ray Diffraction 3.6673 3.7155 -- 336 6795 0.2251 0.2703 -- 100.0
X Ray Diffraction 3.7155 3.7664 -- 364 6773 0.2084 0.274 -- 100.0
X Ray Diffraction 3.7664 3.8202 -- 366 6726 0.1993 0.2358 -- 100.0
X Ray Diffraction 3.8202 3.8772 -- 404 6709 0.1883 0.2348 -- 100.0
X Ray Diffraction 3.8772 3.9378 -- 364 6785 0.1737 0.2307 -- 100.0
X Ray Diffraction 3.9378 4.0023 -- 371 6723 0.1674 0.2204 -- 100.0
X Ray Diffraction 4.0023 4.0713 -- 344 6779 0.1702 0.227 -- 100.0
X Ray Diffraction 4.0713 4.1453 -- 384 6756 0.154 0.1973 -- 100.0
X Ray Diffraction 4.1453 4.225 -- 337 6790 0.1514 0.198 -- 100.0
X Ray Diffraction 4.225 4.3112 -- 346 6782 0.1481 0.1978 -- 100.0
X Ray Diffraction 4.3112 4.4048 -- 372 6763 0.1394 0.1968 -- 100.0
X Ray Diffraction 4.4048 4.5072 -- 306 6852 0.1353 0.1744 -- 100.0
X Ray Diffraction 4.5072 4.6199 -- 350 6797 0.1337 0.1708 -- 100.0
X Ray Diffraction 4.6199 4.7447 -- 371 6760 0.1284 0.1718 -- 100.0
X Ray Diffraction 4.7447 4.8842 -- 347 6828 0.1308 0.176 -- 100.0
X Ray Diffraction 4.8842 5.0417 -- 333 6809 0.1325 0.1773 -- 100.0
X Ray Diffraction 5.0417 5.2217 -- 381 6803 0.1289 0.1717 -- 100.0
X Ray Diffraction 5.2217 5.4305 -- 368 6830 0.128 0.1843 -- 100.0
X Ray Diffraction 5.4305 5.6774 -- 343 6864 0.1255 0.1781 -- 100.0
X Ray Diffraction 5.6774 5.9762 -- 343 6869 0.128 0.1685 -- 100.0
X Ray Diffraction 5.9762 6.35 -- 381 6829 0.1306 0.1897 -- 100.0
X Ray Diffraction 6.35 6.8391 -- 368 6865 0.1314 0.1687 -- 100.0
X Ray Diffraction 6.8391 7.5253 -- 357 6913 0.1305 0.1811 -- 100.0
X Ray Diffraction 7.5253 8.6093 -- 383 6945 0.1425 0.1908 -- 100.0
X Ray Diffraction 8.6093 10.8285 -- 369 6979 0.1568 0.1815 -- 100.0
X Ray Diffraction 10.8285 49.8459 -- 410 7193 0.2054 0.2248 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 116.778
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.987
f_plane_restr 0.007
f_chiral_restr 0.078
f_angle_d 1.439
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19093
Nucleic Acid Atoms 32550
Heterogen Atoms 453
Solvent Atoms 1577

Software

Computing
Computing Package Purpose
XDS 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