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 = 48.32 α = 90
b = 75.34 β = 93.22
c = 52.76 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
1.73 48.24 95.3 0.056 -- -- -- -- 37589 -- -3.0 22.137
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)
1.73 1.82 97.8 0.356 -- 3.0 -- --

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 1.73 48.244 -- 1.99 -- 37583 1499 95.25 -- 0.1694 0.1684 0.194 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 1.73 1.7859 -- 142 3359 0.2408 0.271 -- 98.0
X Ray Diffraction 1.7859 1.8497 -- 142 3322 0.2166 0.2485 -- 97.0
X Ray Diffraction 1.8497 1.9237 -- 138 3340 0.1852 0.259 -- 97.0
X Ray Diffraction 1.9237 2.0113 -- 142 3333 0.1744 0.1973 -- 97.0
X Ray Diffraction 2.0113 2.1173 -- 133 3312 0.1558 0.2008 -- 96.0
X Ray Diffraction 2.1173 2.25 -- 133 3275 0.156 0.1911 -- 96.0
X Ray Diffraction 2.25 2.4237 -- 140 3314 0.1565 0.2087 -- 96.0
X Ray Diffraction 2.4237 2.6676 -- 135 3260 0.1654 0.1959 -- 95.0
X Ray Diffraction 2.6676 3.0536 -- 132 3230 0.173 0.1854 -- 93.0
X Ray Diffraction 3.0536 3.8469 -- 133 3186 0.1558 0.1769 -- 92.0
X Ray Diffraction 3.8469 48.2625 -- 129 3153 0.16 0.1558 -- 90.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.7954
Anisotropic B[1][1] -1.1573
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.4489
Anisotropic B[2][2] 1.1863
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.0291
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.054
f_plane_restr 0.003
f_chiral_restr 0.058
f_angle_d 0.974
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2736
Nucleic Acid Atoms 0
Heterogen Atoms 90
Solvent Atoms 286

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