X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 0.1 M HEPES pH 7.0, 30% Jeffamine ED-2001 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.68 α = 90
b = 55.03 β = 114.09
c = 46.67 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
CCD MARMOSAIC 300 mm CCD -- 2012-10-12
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G

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
1.05 30 99.2 -- 0.044 -- 6.5 -- 91003 0.0 -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)
1.05 1.07 94.2 -- 0.607 2.58 5.1 4332

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 1.05 23.072 -- 1.34 -- 90970 1999 99.1 -- 0.1662 0.1659 0.1793 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 1.0502 1.0765 -- 133 5983 0.2657 0.2949 -- 93.0
X Ray Diffraction 1.0765 1.1056 -- 145 6368 0.2331 0.2563 -- 99.0
X Ray Diffraction 1.1056 1.1381 -- 142 6352 0.2059 0.2229 -- 100.0
X Ray Diffraction 1.1381 1.1749 -- 146 6365 0.1925 0.1867 -- 100.0
X Ray Diffraction 1.1749 1.2169 -- 137 6411 0.1823 0.1961 -- 100.0
X Ray Diffraction 1.2169 1.2656 -- 149 6405 0.1759 0.1927 -- 100.0
X Ray Diffraction 1.2656 1.3232 -- 141 6343 0.1708 0.2073 -- 100.0
X Ray Diffraction 1.3232 1.3929 -- 151 6435 0.1713 0.1705 -- 100.0
X Ray Diffraction 1.3929 1.4802 -- 136 6389 0.1646 0.1926 -- 100.0
X Ray Diffraction 1.4802 1.5944 -- 149 6397 0.1559 0.1847 -- 100.0
X Ray Diffraction 1.5944 1.7549 -- 138 6418 0.1556 0.1738 -- 100.0
X Ray Diffraction 1.7549 2.0087 -- 146 6425 0.157 0.1898 -- 100.0
X Ray Diffraction 2.0087 2.5302 -- 146 6459 0.1543 0.1624 -- 100.0
X Ray Diffraction 2.5302 23.0779 -- 140 6221 0.1606 0.1617 -- 95.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.008
f_chiral_restr 0.093
f_dihedral_angle_d 13.655
f_angle_d 1.457
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1812
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 337

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
PHENIX (phenix.autosol) Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1168) refinement
PHENIX version: (phenix.autosol) model building
HKL-3000 data collection