X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 277.0
Details 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.37 α = 90
b = 75.4 β = 93.32
c = 52.7 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 ADSC QUANTUM 315r -- 2010-12-09
Diffraction Radiation
Monochromator Protocol
two flat Si(111) crystals, mounted in a model DCM from Khozu SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1

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
1.6 48.29 95.9 0.066 -- -- -- -- 48062 -- -3.0 19.275
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)
1.6 1.69 98.3 0.365 -- 3.1 -- --

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 1.6 48.289 -- 1.99 -- 48060 1918 96.5 -- 0.1804 0.1794 0.2042 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 1.6 1.64 -- 138 3322 0.2309 0.2431 -- 98.0
X Ray Diffraction 1.64 1.6844 -- 139 3326 0.2185 0.2311 -- 98.0
X Ray Diffraction 1.6844 1.7339 -- 140 3359 0.1949 0.2465 -- 98.0
X Ray Diffraction 1.7339 1.7899 -- 141 3313 0.1926 0.2363 -- 98.0
X Ray Diffraction 1.7899 1.8539 -- 139 3331 0.1787 0.196 -- 98.0
X Ray Diffraction 1.8539 1.9281 -- 138 3329 0.1704 0.1936 -- 97.0
X Ray Diffraction 1.9281 2.0159 -- 136 3314 0.1726 0.2144 -- 97.0
X Ray Diffraction 2.0159 2.1221 -- 135 3318 0.1667 0.2089 -- 97.0
X Ray Diffraction 2.1221 2.2551 -- 139 3295 0.1709 0.2015 -- 97.0
X Ray Diffraction 2.2551 2.4292 -- 141 3324 0.1722 0.1901 -- 96.0
X Ray Diffraction 2.4292 2.6737 -- 134 3278 0.1796 0.2169 -- 96.0
X Ray Diffraction 2.6737 3.0605 -- 132 3254 0.1868 0.2082 -- 95.0
X Ray Diffraction 3.0605 3.8556 -- 136 3213 0.1682 0.184 -- 94.0
X Ray Diffraction 3.8556 48.3109 -- 130 3166 0.176 0.1885 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.667
Anisotropic B[1][1] -1.7287
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.0993
Anisotropic B[2][2] 1.0666
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.662
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.096
f_plane_restr 0.007
f_chiral_restr 0.085
f_angle_d 1.396
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2768
Nucleic Acid Atoms 0
Heterogen Atoms 81
Solvent Atoms 285

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XSCALE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction