X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 293.15
Details Hepes, KCl, MgCl2, NH4Cl, MPD, EtOH, Spermidine

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 280.92 α = 90
b = 280.92 β = 90
c = 875.59 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2012-11-03
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2

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
3.43 50 92.1 0.152 -- 10.516 8.3 -- 253918 -- -- 98.31
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)
3.43 3.47 78.9 0.744 -- -- 3.4 7175

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 3.43 49.539 -- 1.35 -- 253650 12763 91.83 -- 0.2061 0.2042 0.242 Random selection
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 3.4062 3.4449 -- 342 6189 0.2977 0.3235 -- 72.0
X Ray Diffraction 3.4449 3.4854 -- 378 7414 0.2921 0.3266 -- 86.0
X Ray Diffraction 3.4854 3.5279 -- 434 7649 0.2729 0.3207 -- 89.0
X Ray Diffraction 3.5279 3.5725 -- 427 7741 0.2641 0.2905 -- 90.0
X Ray Diffraction 3.5725 3.6195 -- 393 7789 0.2576 0.308 -- 90.0
X Ray Diffraction 3.6195 3.6691 -- 407 7943 0.2496 0.2758 -- 92.0
X Ray Diffraction 3.6691 3.7215 -- 414 7969 0.2354 0.2898 -- 92.0
X Ray Diffraction 3.7215 3.777 -- 458 7943 0.2352 0.2863 -- 92.0
X Ray Diffraction 3.777 3.836 -- 424 8024 0.2311 0.28 -- 93.0
X Ray Diffraction 3.836 3.8989 -- 395 8082 0.2126 0.2649 -- 93.0
X Ray Diffraction 3.8989 3.9661 -- 394 8045 0.2152 0.2475 -- 93.0
X Ray Diffraction 3.9661 4.0382 -- 434 8031 0.2037 0.2458 -- 93.0
X Ray Diffraction 4.0382 4.1158 -- 446 8066 0.2074 0.2391 -- 93.0
X Ray Diffraction 4.1158 4.1998 -- 429 8118 0.2031 0.2612 -- 93.0
X Ray Diffraction 4.1998 4.2911 -- 461 8043 0.1962 0.2523 -- 93.0
X Ray Diffraction 4.2911 4.3908 -- 399 8111 0.1922 0.2321 -- 93.0
X Ray Diffraction 4.3908 4.5006 -- 423 8131 0.1902 0.2283 -- 94.0
X Ray Diffraction 4.5006 4.6222 -- 434 8112 0.1831 0.2259 -- 93.0
X Ray Diffraction 4.6222 4.7581 -- 429 8137 0.1758 0.2299 -- 93.0
X Ray Diffraction 4.7581 4.9115 -- 449 8105 0.1754 0.2209 -- 93.0
X Ray Diffraction 4.9115 5.0869 -- 449 8097 0.1771 0.2261 -- 93.0
X Ray Diffraction 5.0869 5.2903 -- 426 8113 0.1691 0.2179 -- 93.0
X Ray Diffraction 5.2903 5.5308 -- 436 8149 0.1571 0.2094 -- 93.0
X Ray Diffraction 5.5308 5.822 -- 428 8095 0.1562 0.1881 -- 92.0
X Ray Diffraction 5.822 6.1861 -- 411 8160 0.1628 0.2122 -- 92.0
X Ray Diffraction 6.1861 6.6627 -- 420 8215 0.1706 0.2143 -- 93.0
X Ray Diffraction 6.6627 7.3313 -- 457 8109 0.1638 0.2096 -- 92.0
X Ray Diffraction 7.3313 8.3877 -- 409 8128 0.1741 0.23 -- 91.0
X Ray Diffraction 8.3877 10.5508 -- 448 8735 0.1957 0.2348 -- 96.0
X Ray Diffraction 10.5508 49.5444 -- 509 9444 0.2622 0.2597 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 80.29
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.099
f_bond_d 0.006
f_plane_restr 0.006
f_chiral_restr 0.058
f_dihedral_angle_d 16.937
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19929
Nucleic Acid Atoms 60464
Heterogen Atoms 791
Solvent Atoms 0

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
PDB_EXTRACT data extraction version: 3.15
DENZO data reduction