X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9.5
Temperature 293.0
Details 200mM NaCl, 14% Isopropanol, 2mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP HCl)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.39 α = 90
b = 77.39 β = 90
c = 147.01 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2016-04-25
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 1.1808 SSRL BL14-1

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
1.8 50 99.9 0.071 -- 27.5 6.7 -- 48010 -- -- 22.03
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)
1.8 1.83 100.0 -- 0.673 3.5 6.6 2339

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 1.8 39.557 -- 1.35 -- 47977 2000 99.92 -- 0.1547 0.1536 0.1789 --
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 1.7998 1.8448 -- 141 3253 0.2027 0.2304 0.0 100.0
X Ray Diffraction 1.8448 1.8946 -- 139 3218 0.1925 0.1971 0.0 100.0
X Ray Diffraction 1.8946 1.9504 -- 142 3243 0.1978 0.2633 0.0 100.0
X Ray Diffraction 1.9504 2.0134 -- 141 3234 0.1619 0.1813 0.0 100.0
X Ray Diffraction 2.0134 2.0853 -- 142 3243 0.156 0.1614 0.0 100.0
X Ray Diffraction 2.0853 2.1688 -- 141 3257 0.1512 0.1806 0.0 100.0
X Ray Diffraction 2.1688 2.2675 -- 144 3264 0.1637 0.1986 0.0 100.0
X Ray Diffraction 2.2675 2.387 -- 142 3244 0.1568 0.1929 0.0 100.0
X Ray Diffraction 2.387 2.5366 -- 142 3272 0.1594 0.1974 0.0 100.0
X Ray Diffraction 2.5366 2.7324 -- 143 3300 0.1548 0.1756 0.0 100.0
X Ray Diffraction 2.7324 3.0072 -- 146 3295 0.1526 0.164 0.0 100.0
X Ray Diffraction 3.0072 3.4422 -- 141 3323 0.1476 0.1794 0.0 100.0
X Ray Diffraction 3.4422 4.3359 -- 146 3353 0.135 0.1656 0.0 100.0
X Ray Diffraction 4.3359 39.5666 -- 150 3478 0.1488 0.1608 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.1589
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.055
f_dihedral_angle_d 13.404
f_bond_d 0.008
f_angle_d 0.868
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3024
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 272

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHENIX refinement version: 1.10_2155
PDB_EXTRACT data extraction version: 3.22
HKL-2000 data reduction
PHASER phasing