X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 293.0
Details 16% PEG3350, 12% isopropanol, saturated L-tryptophan, 0.1 M Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.21 α = 90
b = 106.75 β = 107.01
c = 68.34 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 -- 2012-01-30
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1

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
2.89 65.35 97.9 0.058 -- -- 3.4 19450 19005 -- -- --
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)
2.893 3.05 -- 0.286 -- 2.6 3.2 --

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 2.899 39.045 -- 1.34 -- 18863 955 97.62 -- 0.2118 0.2098 0.2488 --
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 2.899 3.0523 -- 131 2459 0.2868 0.319 -- 94.0
X Ray Diffraction 3.0523 3.2434 -- 153 2554 0.2538 0.329 -- 99.0
X Ray Diffraction 3.2434 3.4937 -- 113 2566 0.2498 0.2818 -- 97.0
X Ray Diffraction 3.4937 3.845 -- 124 2583 0.209 0.2542 -- 99.0
X Ray Diffraction 3.845 4.4007 -- 150 2545 0.1918 0.2313 -- 98.0
X Ray Diffraction 4.4007 5.542 -- 138 2600 0.1787 0.2016 -- 99.0
X Ray Diffraction 5.542 39.0483 -- 146 2601 0.1979 0.2414 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.053
f_dihedral_angle_d 14.531
f_angle_d 0.787
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6380
Nucleic Acid Atoms 191
Heterogen Atoms 28
Solvent Atoms 7

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement