X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 10% PEG 4000, 20% glycerol, 0.1 M MES/imidazole, 0.02 M of each alcohol (1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.5 α = 90
b = 165.4 β = 90
c = 166.21 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2012-11-22
Diffraction Radiation
Monochromator Protocol
GRAPHITE, SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1

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
1.8 45 95.7 0.071 -- -- 3.2 -- 134076 -- -3.0 24.48
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)
1.8 1.9 76.7 0.542 -- 2.06 -- --

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 1.8 41.553 -- 1.36 -- 133973 6700 95.71 -- 0.1749 0.1735 0.2029 Random
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 1.8 1.8205 -- 170 3218 0.2812 0.355 -- 72.0
X Ray Diffraction 1.8205 1.8419 -- 168 3191 0.2567 0.2938 -- 74.0
X Ray Diffraction 1.8419 1.8643 -- 169 3211 0.2429 0.2693 -- 73.0
X Ray Diffraction 1.8643 1.8879 -- 176 3347 0.2368 0.2864 -- 76.0
X Ray Diffraction 1.8879 1.9128 -- 229 4335 0.2365 0.2812 -- 100.0
X Ray Diffraction 1.9128 1.939 -- 232 4414 0.2374 0.2821 -- 100.0
X Ray Diffraction 1.939 1.9667 -- 228 4337 0.2263 0.291 -- 100.0
X Ray Diffraction 1.9667 1.996 -- 231 4389 0.2191 0.2491 -- 100.0
X Ray Diffraction 1.996 2.0272 -- 234 4435 0.2088 0.2519 -- 100.0
X Ray Diffraction 2.0272 2.0605 -- 229 4341 0.199 0.253 -- 100.0
X Ray Diffraction 2.0605 2.096 -- 234 4443 0.1892 0.2479 -- 100.0
X Ray Diffraction 2.096 2.1341 -- 228 4345 0.1866 0.2402 -- 100.0
X Ray Diffraction 2.1341 2.1752 -- 233 4422 0.1809 0.2133 -- 100.0
X Ray Diffraction 2.1752 2.2196 -- 229 4352 0.1811 0.2288 -- 100.0
X Ray Diffraction 2.2196 2.2678 -- 234 4446 0.1825 0.2149 -- 100.0
X Ray Diffraction 2.2678 2.3206 -- 229 4353 0.1782 0.2116 -- 100.0
X Ray Diffraction 2.3206 2.3786 -- 234 4425 0.1751 0.2002 -- 100.0
X Ray Diffraction 2.3786 2.4429 -- 229 4382 0.1705 0.2072 -- 100.0
X Ray Diffraction 2.4429 2.5148 -- 232 4402 0.1742 0.2198 -- 100.0
X Ray Diffraction 2.5148 2.5959 -- 234 4441 0.1697 0.2071 -- 100.0
X Ray Diffraction 2.5959 2.6887 -- 229 4360 0.1672 0.2022 -- 99.0
X Ray Diffraction 2.6887 2.7963 -- 232 4406 0.1666 0.1845 -- 99.0
X Ray Diffraction 2.7963 2.9236 -- 232 4399 0.1738 0.1996 -- 99.0
X Ray Diffraction 2.9236 3.0776 -- 231 4391 0.1667 0.198 -- 99.0
X Ray Diffraction 3.0776 3.2704 -- 229 4359 0.1664 0.1785 -- 98.0
X Ray Diffraction 3.2704 3.5228 -- 229 4352 0.174 0.2124 -- 97.0
X Ray Diffraction 3.5228 3.8771 -- 231 4371 0.157 0.1871 -- 97.0
X Ray Diffraction 3.8771 4.4375 -- 230 4362 0.1467 0.1625 -- 97.0
X Ray Diffraction 4.4375 5.5887 -- 235 4464 0.1484 0.1638 -- 97.0
X Ray Diffraction 5.5887 41.5636 -- 240 4580 0.1671 0.1801 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.3083
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_angle_d 1.044
f_bond_d 0.008
f_chiral_restr 0.066
f_dihedral_angle_d 14.197
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9061
Nucleic Acid Atoms 0
Heterogen Atoms 106
Solvent Atoms 1051

Software

Software
Software Name Purpose
PHENIX refinement
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.20
PHASER phasing version: 2.6
XDS data reduction