X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 0.05 M Na-cacodylate, 2.5 mM spermine, 60 mM magnesium chloride, 3 % PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.28 α = 90
b = 111.89 β = 90
c = 117.78 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2013-03-14
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.97626 PETRA III, EMBL C/O DESY P14 (MX2)

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
3.07 999 98.6 -- -- -- -- 10913 10762 2.0 2.0 --
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)
3.07 3.25 91.7 -- -- -- -- --

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 3.0754 68.325 -- 2.03 -- 10739 538 98.53 -- 0.2547 0.2545 0.258 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 3.0754 3.3849 -- 126 2396 0.3143 0.3338 -- 95.0
X Ray Diffraction 3.3849 3.8747 -- 134 2544 0.2853 0.3046 -- 100.0
X Ray Diffraction 3.8747 4.8815 -- 136 2578 0.2528 0.2502 -- 100.0
X Ray Diffraction 4.8815 68.3422 -- 142 2683 0.2345 0.2327 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.058
f_dihedral_angle_d 24.454
f_angle_d 0.888
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2899
Nucleic Acid Atoms 555
Heterogen Atoms 65
Solvent Atoms 2

Software

Computing
Computing Package Purpose
mxCuBE Hamburg Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
PHASER model building
mxCuBE version: Hamburg data collection