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 = 401.25 α = 90
b = 401.25 β = 90
c = 176.04 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
3.3 35 98.9 0.097 -- -- 3.8 210600 210600 -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)
3.297 3.42 99.3 0.731 -- -- 3.8 20935

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 3.297 34.55 -- 1.33 210495 210495 10598 98.35 -- 0.1654 0.1632 0.2076 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 3.297 3.3345 -- 297 5518 0.2904 0.3303 -- 82.0
X Ray Diffraction 3.3345 3.3737 -- 345 6666 0.2813 0.3232 -- 99.0
X Ray Diffraction 3.3737 3.4148 -- 381 6624 0.2739 0.3095 -- 100.0
X Ray Diffraction 3.4148 3.458 -- 353 6709 0.2727 0.3316 -- 100.0
X Ray Diffraction 3.458 3.5034 -- 365 6702 0.2538 0.3107 -- 100.0
X Ray Diffraction 3.5034 3.5514 -- 405 6600 0.2439 0.2746 -- 100.0
X Ray Diffraction 3.5514 3.602 -- 350 6728 0.2297 0.2715 -- 100.0
X Ray Diffraction 3.602 3.6558 -- 342 6716 0.2188 0.2678 -- 100.0
X Ray Diffraction 3.6558 3.7128 -- 385 6659 0.2104 0.2425 -- 100.0
X Ray Diffraction 3.7128 3.7736 -- 374 6637 0.1947 0.2517 -- 100.0
X Ray Diffraction 3.7736 3.8386 -- 315 6818 0.1858 0.2193 -- 100.0
X Ray Diffraction 3.8386 3.9083 -- 360 6660 0.1854 0.2469 -- 100.0
X Ray Diffraction 3.9083 3.9834 -- 338 6715 0.1765 0.2201 -- 100.0
X Ray Diffraction 3.9834 4.0646 -- 377 6692 0.1696 0.2227 -- 100.0
X Ray Diffraction 4.0646 4.1528 -- 348 6690 0.1556 0.2009 -- 100.0
X Ray Diffraction 4.1528 4.2492 -- 350 6728 0.1526 0.2173 -- 100.0
X Ray Diffraction 4.2492 4.3553 -- 370 6676 0.1463 0.1843 -- 99.0
X Ray Diffraction 4.3553 4.4728 -- 371 6701 0.1411 0.1845 -- 99.0
X Ray Diffraction 4.4728 4.6041 -- 358 6730 0.1362 0.1888 -- 99.0
X Ray Diffraction 4.6041 4.7524 -- 317 6738 0.1342 0.1803 -- 99.0
X Ray Diffraction 4.7524 4.9218 -- 349 6709 0.124 0.1825 -- 99.0
X Ray Diffraction 4.9218 5.1182 -- 342 6706 0.1253 0.1658 -- 99.0
X Ray Diffraction 5.1182 5.3504 -- 352 6778 0.1235 0.1678 -- 99.0
X Ray Diffraction 5.3504 5.6313 -- 346 6710 0.1309 0.1979 -- 99.0
X Ray Diffraction 5.6313 5.9824 -- 354 6756 0.1358 0.1842 -- 99.0
X Ray Diffraction 5.9824 6.4416 -- 333 6753 0.142 0.1905 -- 99.0
X Ray Diffraction 6.4416 7.0848 -- 359 6775 0.1391 0.1975 -- 99.0
X Ray Diffraction 7.0848 8.0985 -- 342 6774 0.1331 0.1767 -- 98.0
X Ray Diffraction 8.0985 10.16 -- 367 6697 0.1536 0.1813 -- 97.0
X Ray Diffraction 10.16 34.5517 -- 353 6532 0.1938 0.2149 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 131.624
Anisotropic B[1][1] -4.1015
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.1015
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.9121
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.997
f_plane_restr 0.005
f_chiral_restr 0.067
f_angle_d 0.979
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19088
Nucleic Acid Atoms 32508
Heterogen Atoms 322
Solvent Atoms 568

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