X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 289.0
Details 4.8%(v/v) isopropanol, 0.096 M tacsimate, 1.92-1.95 M ammonium sulfate, and 10-11%(v/v) glycerol and then gradually exchanged into a cryo stabilizer solution containing 4.8%(v/v) isopropanol, 0.096 M tacsimate, 1.95 M ammonium sulfate and 19-27%(v/v) xylitol with CTP prior to freezing, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.49 α = 73.65
b = 64.37 β = 73.56
c = 102.29 γ = 72.2
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NOIR-1 -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2

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
2.69 42.38 97.9 0.05 -- -- 1.99 -- 39877 2.0 1.5 --
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)
2.69 2.79 98.0 0.456 -- 1.5 1.98 3951

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 2.69 42.376 -- 1.96 -- 39801 2022 97.75 -- 0.2151 0.2128 0.2562 --
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 2.69 2.7573 -- 134 2662 0.3429 0.3472 -- 98.0
X Ray Diffraction 2.7573 2.8318 -- 148 2752 0.3269 0.3969 -- 98.0
X Ray Diffraction 2.8318 2.9151 -- 133 2733 0.3137 0.3333 -- 98.0
X Ray Diffraction 2.9151 3.0092 -- 145 2662 0.2989 0.364 -- 98.0
X Ray Diffraction 3.0092 3.1167 -- 152 2721 0.2983 0.3751 -- 98.0
X Ray Diffraction 3.1167 3.2415 -- 157 2724 0.2891 0.3666 -- 99.0
X Ray Diffraction 3.2415 3.3889 -- 134 2749 0.2659 0.3197 -- 98.0
X Ray Diffraction 3.3889 3.5675 -- 129 2660 0.278 0.2972 -- 96.0
X Ray Diffraction 3.5675 3.7909 -- 147 2680 0.2621 0.3236 -- 97.0
X Ray Diffraction 3.7909 4.0834 -- 154 2598 0.2028 0.2642 -- 96.0
X Ray Diffraction 4.0834 4.4939 -- 141 2747 0.1624 0.2019 -- 99.0
X Ray Diffraction 4.4939 5.1432 -- 164 2691 0.1659 0.2166 -- 99.0
X Ray Diffraction 5.1432 6.4762 -- 146 2735 0.1793 0.2277 -- 98.0
X Ray Diffraction 6.4762 42.3812 -- 138 2665 0.1712 0.1806 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 81.9612
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.722
f_plane_restr 0.007
f_chiral_restr 0.049
f_angle_d 1.217
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7400
Nucleic Acid Atoms 1520
Heterogen Atoms 0
Solvent Atoms 109

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
DTREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.9.9.1L data reduction
D*trek data collection