X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 7
Temperature 291.0
Details 80mM NaCl, 20mM MgCl2, 40mM sodium cacodylate, 12mM spermine, 10% 2-methyl-1,3 propanediol, pH 7.0, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.84 α = 90
b = 205.18 β = 90
c = 161.42 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2013-03-07
Diffraction Radiation
Monochromator Protocol
Cryogenically-cooled single crystal Si(220) side bounce monochromator. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E

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
3.2 50 98.8 0.16 -- -- 6.9 -- 26207 -- -- 74.54
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)
3.2 3.26 96.9 -- -- 2.29 6.1 1289

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 3.2 43.292 -- 1.33 -- 25268 2512 97.85 -- 0.2406 0.2364 0.2783 --
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 3.2001 3.2616 -- 134 1176 0.342 0.3608 -- 94.0
X Ray Diffraction 3.2616 3.3281 -- 136 1213 0.3402 0.3719 -- 94.0
X Ray Diffraction 3.3281 3.4005 -- 135 1205 0.3413 0.3437 -- 96.0
X Ray Diffraction 3.4005 3.4796 -- 132 1195 0.3347 0.3443 -- 95.0
X Ray Diffraction 3.4796 3.5665 -- 138 1243 0.3313 0.3621 -- 97.0
X Ray Diffraction 3.5665 3.6629 -- 135 1244 0.321 0.3602 -- 97.0
X Ray Diffraction 3.6629 3.7706 -- 141 1250 0.3057 0.3581 -- 98.0
X Ray Diffraction 3.7706 3.8923 -- 138 1264 0.2659 0.325 -- 98.0
X Ray Diffraction 3.8923 4.0313 -- 134 1268 0.2664 0.3028 -- 99.0
X Ray Diffraction 4.0313 4.1926 -- 134 1258 0.275 0.3382 -- 99.0
X Ray Diffraction 4.1926 4.3832 -- 139 1283 0.2687 0.3519 -- 99.0
X Ray Diffraction 4.3832 4.614 -- 137 1276 0.2573 0.3099 -- 99.0
X Ray Diffraction 4.614 4.9028 -- 148 1289 0.248 0.2822 -- 100.0
X Ray Diffraction 4.9028 5.2807 -- 143 1281 0.2144 0.2321 -- 100.0
X Ray Diffraction 5.2807 5.811 -- 142 1313 0.2025 0.2744 -- 100.0
X Ray Diffraction 5.811 6.6492 -- 146 1317 0.2229 0.2494 -- 100.0
X Ray Diffraction 6.6492 8.3674 -- 147 1321 0.2085 0.2291 -- 100.0
X Ray Diffraction 8.3674 43.2959 -- 153 1360 0.1706 0.2178 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 141.604
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.951
f_plane_restr 0.002
f_chiral_restr 0.019
f_angle_d 0.458
f_bond_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 6832
Heterogen Atoms 18
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
SCALEPACK data reduction