X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 277.15
Details 5 mM Mes-Bis-Tris, 75 mM lithium chloride, 1 mM DTT, 0.1 mM sodium EDTA, 0.25 mM Mega 8, 0.7 mM peptidic ligand, 16 % v/v methanol/water in reservoir

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.07 α = 90
b = 72.66 β = 90
c = 110.67 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
PIXEL DECTRIS PILATUS 6M -- 2015-10-24
Diffraction Radiation
Monochromator Protocol
-- 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
1.56 44.02 98.8 -- 0.045 -- 5.5 -- 67994 -- -- --
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)
1.56 1.65 96.7 -- 0.496 3.1 5.5 --

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 1.56 44.022 -- 1.35 -- 67941 3397 98.84 -- 0.1422 0.1405 0.1766 Random Selection
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 1.5581 1.5803 -- 126 2405 0.1817 0.2582 -- 91.0
X Ray Diffraction 1.5803 1.6039 -- 141 2676 0.1686 0.1941 -- 99.0
X Ray Diffraction 1.6039 1.629 -- 140 2644 0.1466 0.2465 -- 99.0
X Ray Diffraction 1.629 1.6557 -- 139 2644 0.1391 0.2026 -- 99.0
X Ray Diffraction 1.6557 1.6842 -- 141 2682 0.1306 0.2048 -- 99.0
X Ray Diffraction 1.6842 1.7149 -- 139 2643 0.1258 0.1724 -- 99.0
X Ray Diffraction 1.7149 1.7479 -- 141 2674 0.1161 0.1967 -- 99.0
X Ray Diffraction 1.7479 1.7835 -- 140 2677 0.1184 0.1734 -- 99.0
X Ray Diffraction 1.7835 1.8223 -- 139 2652 0.1182 0.1909 -- 99.0
X Ray Diffraction 1.8223 1.8647 -- 143 2713 0.1172 0.166 -- 99.0
X Ray Diffraction 1.8647 1.9113 -- 140 2683 0.1217 0.1649 -- 99.0
X Ray Diffraction 1.9113 1.963 -- 142 2689 0.126 0.1891 -- 100.0
X Ray Diffraction 1.963 2.0208 -- 141 2679 0.1245 0.189 -- 99.0
X Ray Diffraction 2.0208 2.086 -- 142 2700 0.1259 0.1588 -- 100.0
X Ray Diffraction 2.086 2.1606 -- 141 2674 0.1306 0.1764 -- 99.0
X Ray Diffraction 2.1606 2.2471 -- 143 2716 0.1271 0.1756 -- 100.0
X Ray Diffraction 2.2471 2.3493 -- 143 2705 0.1256 0.1726 -- 99.0
X Ray Diffraction 2.3493 2.4732 -- 142 2709 0.1305 0.1756 -- 100.0
X Ray Diffraction 2.4732 2.6281 -- 144 2722 0.1353 0.1838 -- 100.0
X Ray Diffraction 2.6281 2.831 -- 144 2737 0.1464 0.1805 -- 99.0
X Ray Diffraction 2.831 3.1158 -- 144 2738 0.1505 0.1663 -- 100.0
X Ray Diffraction 3.1158 3.5665 -- 145 2749 0.1578 0.1797 -- 99.0
X Ray Diffraction 3.5665 4.4927 -- 145 2773 0.1384 0.1471 -- 99.0
X Ray Diffraction 4.4927 44.0399 -- 152 2860 0.1604 0.1881 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_bond_d 0.01
f_dihedral_angle_d 13.974
f_chiral_restr 0.06
f_angle_d 1.035
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2941
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 364

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10.1_2155: ???)
XDS data reduction
PHASER phasing
Coot model building
XDS data scaling