X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 294.0
Details 100 mM Tris-HCl, 13-15% PEG 4000, 200 mM MgCl2, 6.25% PEG 400

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.34 α = 90
b = 82.91 β = 108.78
c = 129.08 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2015-04-16
Diffraction Radiation
Monochromator Protocol
Si 220 filter SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 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
2.5 49.65 98.73 0.1287 -- -- 3.4 254270 254270 -- -- 47.68
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)
2.5 2.589 97.59 -- -- 1.12 -- --

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 2.5 49.65 -- 1.02 -- 140650 7077 95.59 -- 0.2246 0.2232 0.2508 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 2.5 2.5284 -- 206 4287 0.3793 0.3997 -- 90.0
X Ray Diffraction 2.5284 2.5582 -- 199 4175 0.3632 0.4325 -- 92.0
X Ray Diffraction 2.5582 2.5894 -- 236 4444 0.3549 0.3567 -- 95.0
X Ray Diffraction 2.5894 2.6222 -- 283 4456 0.3507 0.3699 -- 96.0
X Ray Diffraction 2.6222 2.6567 -- 238 4498 0.343 0.3394 -- 97.0
X Ray Diffraction 2.6567 2.693 -- 202 4582 0.3426 0.3594 -- 97.0
X Ray Diffraction 2.693 2.7315 -- 227 4531 0.333 0.341 -- 97.0
X Ray Diffraction 2.7315 2.7723 -- 214 4543 0.3356 0.3158 -- 97.0
X Ray Diffraction 2.7723 2.8156 -- 226 4367 0.3145 0.3496 -- 96.0
X Ray Diffraction 2.8156 2.8618 -- 252 4571 0.2927 0.3101 -- 96.0
X Ray Diffraction 2.8618 2.9111 -- 255 4424 0.3011 0.2976 -- 96.0
X Ray Diffraction 2.9111 2.964 -- 267 4483 0.2907 0.3363 -- 95.0
X Ray Diffraction 2.964 3.021 -- 208 4404 0.2771 0.2852 -- 95.0
X Ray Diffraction 3.021 3.0827 -- 248 4412 0.2816 0.3113 -- 94.0
X Ray Diffraction 3.0827 3.1497 -- 249 4244 0.2874 0.3239 -- 92.0
X Ray Diffraction 3.1497 3.223 -- 242 4474 0.2797 0.2427 -- 97.0
X Ray Diffraction 3.223 3.3035 -- 228 4569 0.2576 0.336 -- 97.0
X Ray Diffraction 3.3035 3.3928 -- 243 4511 0.2394 0.2992 -- 97.0
X Ray Diffraction 3.3928 3.4927 -- 230 4575 0.2223 0.2601 -- 97.0
X Ray Diffraction 3.4927 3.6054 -- 261 4488 0.2085 0.2374 -- 97.0
X Ray Diffraction 3.6054 3.7342 -- 204 4521 0.2066 0.2258 -- 97.0
X Ray Diffraction 3.7342 3.8836 -- 241 4478 0.1984 0.2394 -- 96.0
X Ray Diffraction 3.8836 4.0603 -- 247 4334 0.1868 0.2319 -- 94.0
X Ray Diffraction 4.0603 4.2743 -- 250 4369 0.171 0.1755 -- 94.0
X Ray Diffraction 4.2743 4.5419 -- 280 4517 0.1591 0.1924 -- 97.0
X Ray Diffraction 4.5419 4.8923 -- 244 4523 0.1618 0.1872 -- 97.0
X Ray Diffraction 4.8923 5.3841 -- 215 4521 0.1704 0.1994 -- 97.0
X Ray Diffraction 5.3841 6.1619 -- 225 4373 0.1972 0.239 -- 94.0
X Ray Diffraction 6.1619 7.7586 -- 223 4545 0.1886 0.2392 -- 97.0
X Ray Diffraction 7.7586 49.6621 -- 234 4354 0.1672 0.1901 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 72.8857
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.655
f_bond_d 0.003
f_chiral_restr 0.03
f_angle_d 0.69
f_plane_restr 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 11540
Nucleic Acid Atoms 1640
Heterogen Atoms 106
Solvent Atoms 229

Software

Software
Software Name Purpose
PHENIX refinement
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.15
XDS data reduction
PHASER phasing
Coot model building