X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
Temperature 294.0
Details Protein at 8 mg/mL in buffer containing 50 mM potassium phosphate pH 8.0, 50 mM potassium chloride, and 10 mM choline was mixed in a 1:1 ratio with well solution containing 1.0-1.2 M sodium malonate pH 7.0-8.0.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 229.57 α = 90
b = 229.57 β = 90
c = 78.63 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-08-03
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 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
1.85 50 99.9 -- 0.154 -- 13.0 -- 177264 -- -- --
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)
1.85 1.88 99.9 0.984 -- 3.0 11.4 --

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 1.852 49.483 -- 1.34 -- 177264 5327 99.91 -- 0.1747 0.1737 0.2083 --
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 1.8516 1.8726 -- 100 5730 0.2596 0.2132 -- 100.0
X Ray Diffraction 1.8726 1.8947 -- 307 5528 0.2539 0.3299 -- 100.0
X Ray Diffraction 1.8947 1.9178 -- 0 5873 0.2462 1.0E7 -- 100.0
X Ray Diffraction 1.9178 1.9421 -- 410 5426 0.2399 0.2775 -- 100.0
X Ray Diffraction 1.9421 1.9676 -- 0 5856 0.2289 1.0E7 -- 100.0
X Ray Diffraction 1.9676 1.9946 -- 395 5425 0.2291 0.2346 -- 100.0
X Ray Diffraction 1.9946 2.0231 -- 15 5863 0.2188 0.4203 -- 100.0
X Ray Diffraction 2.0231 2.0533 -- 56 5770 0.2196 0.208 -- 100.0
X Ray Diffraction 2.0533 2.0853 -- 354 5507 0.2076 0.2303 -- 100.0
X Ray Diffraction 2.0853 2.1195 -- 0 5870 0.2125 1.0E7 -- 100.0
X Ray Diffraction 2.1195 2.1561 -- 410 5435 0.2005 0.2362 -- 100.0
X Ray Diffraction 2.1561 2.1953 -- 0 5890 0.2028 1.0E7 -- 100.0
X Ray Diffraction 2.1953 2.2375 -- 410 5479 0.2009 0.2357 -- 100.0
X Ray Diffraction 2.2375 2.2832 -- 0 5834 0.198 1.0E7 -- 100.0
X Ray Diffraction 2.2832 2.3328 -- 42 5853 0.1944 0.2018 -- 100.0
X Ray Diffraction 2.3328 2.3871 -- 368 5533 0.1862 0.2288 -- 100.0
X Ray Diffraction 2.3871 2.4468 -- 0 5858 0.1849 1.0E7 -- 100.0
X Ray Diffraction 2.4468 2.5129 -- 410 5472 0.1802 0.2037 -- 100.0
X Ray Diffraction 2.5129 2.5869 -- 0 5902 0.1833 1.0E7 -- 100.0
X Ray Diffraction 2.5869 2.6704 -- 410 5492 0.187 0.2243 -- 100.0
X Ray Diffraction 2.6704 2.7658 -- 0 5912 0.1838 1.0E7 -- 100.0
X Ray Diffraction 2.7658 2.8765 -- 42 5872 0.1809 0.1349 -- 100.0
X Ray Diffraction 2.8765 3.0074 -- 368 5543 0.1756 0.2245 -- 100.0
X Ray Diffraction 3.0074 3.166 -- 0 5953 0.1655 1.0E7 -- 100.0
X Ray Diffraction 3.166 3.3643 -- 410 5532 0.1565 0.193 -- 100.0
X Ray Diffraction 3.3643 3.624 -- 0 5963 0.1459 1.0E7 -- 100.0
X Ray Diffraction 3.624 3.9885 -- 410 5582 0.1334 0.1638 -- 100.0
X Ray Diffraction 3.9885 4.5653 -- 0 6004 0.1209 1.0E7 -- 99.0
X Ray Diffraction 4.5653 5.7504 -- 410 5677 0.1274 0.1746 -- 100.0
X Ray Diffraction 5.7504 49.5005 -- 0 6303 0.1394 1.0E7 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.075
f_chiral_restr 0.04
f_bond_d 0.008
f_dihedral_angle_d 13.251
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12674
Nucleic Acid Atoms 0
Heterogen Atoms 58
Solvent Atoms 2374

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing