X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 5.5
Temperature 298.0
Details PEG 3350, ammonium sulfate, Bis-Tris , pH 5.5, VAPOR DIFFUSION, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.96 α = 90
b = 70.14 β = 90
c = 225.11 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 -- 2012-05-10
Diffraction Radiation
Monochromator Protocol
LIQUID NITROGEN-COOLED DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.9537 SSRL BL12-2

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
1.49 39.68 99.5 0.142 -- -- -- -- 140662 -3.0 -- --
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)
1.65 1.78 99.3 1.01 -- -- -- --

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 1.65 37.888 -- 1.35 107588 106921 1826 99.38 -- 0.1744 0.1738 0.2034 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 1.65 1.6946 -- 138 8010 0.2176 0.259 -- 99.0
X Ray Diffraction 1.6946 1.7445 -- 139 7940 0.2077 0.2514 -- 99.0
X Ray Diffraction 1.7445 1.8008 -- 138 7978 0.1974 0.2371 -- 99.0
X Ray Diffraction 1.8008 1.8651 -- 139 8002 0.1901 0.2345 -- 100.0
X Ray Diffraction 1.8651 1.9398 -- 139 8003 0.1851 0.2517 -- 100.0
X Ray Diffraction 1.9398 2.0281 -- 139 8002 0.1828 0.2548 -- 100.0
X Ray Diffraction 2.0281 2.135 -- 140 8035 0.1791 0.1825 -- 99.0
X Ray Diffraction 2.135 2.2688 -- 140 8073 0.1748 0.2082 -- 100.0
X Ray Diffraction 2.2688 2.4439 -- 141 8110 0.1736 0.1949 -- 100.0
X Ray Diffraction 2.4439 2.6898 -- 141 8115 0.174 0.2144 -- 100.0
X Ray Diffraction 2.6898 3.0789 -- 142 8131 0.1722 0.1969 -- 99.0
X Ray Diffraction 3.0789 3.8784 -- 143 8242 0.1524 0.1869 -- 100.0
X Ray Diffraction 3.8784 37.8982 -- 147 8454 0.1707 0.1786 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.5521
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.008
f_plane_restr 0.006
f_dihedral_angle_d 13.785
f_chiral_restr 0.076
f_angle_d 1.184
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6606
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 911

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.5.0
PHENIX refinement version: 1.8_1069
PDB_EXTRACT data extraction version: 3.11
XDS data scaling