X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 0.1 M ammonium acetate, 0.1 M Bis-tris, 25% PEG 3350, 30 mM Me-alpha-mannose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 99.77 α = 90
b = 99.77 β = 90
c = 172.37 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 OXFORD ONYX CCD -- 2012-01-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SEALED TUBE OTHER 1.5418 -- --

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
2.85 24.9 99.8 -- 0.211 -- 4.9 23789 23789 -- -- --
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)
2.85 3.0 100.0 0.477 0.477 1.5 4.9 3401

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 2.85 24.895 -- 1.35 -- 23763 1182 99.95 -- 0.1973 0.1946 0.2481 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 2.85 2.9796 -- 144 2777 0.2417 0.3075 -- 100.0
X Ray Diffraction 2.9796 3.1364 -- 142 2775 0.2428 0.3027 -- 100.0
X Ray Diffraction 3.1364 3.3324 -- 159 2777 0.2208 0.2875 -- 100.0
X Ray Diffraction 3.3324 3.589 -- 135 2802 0.1982 0.2745 -- 100.0
X Ray Diffraction 3.589 3.9489 -- 155 2796 0.1805 0.2506 -- 100.0
X Ray Diffraction 3.9489 4.5174 -- 153 2823 0.1631 0.2013 -- 100.0
X Ray Diffraction 4.5174 5.6803 -- 136 2863 0.1617 0.1983 -- 100.0
X Ray Diffraction 5.6803 24.8957 -- 158 2968 0.2013 0.2269 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.7374
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 14.392
f_plane_restr 0.004
f_chiral_restr 0.058
f_angle_d 1.045
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5775
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 0

Software

Computing
Computing Package Purpose
d*TREK Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
SCALA version: 3.3.20 data reduction
D*trek data collection