X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 289.0
Details 4.8%(v/v) isopropanol, 0.096 M tacsimate (Hampton Research), 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 dCTP prior to freezing, pH pH 8.5-9.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.52 α = 73.48
b = 63.47 β = 73.44
c = 101.95 γ = 73.64
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
2.63 47.51 98.0 0.042 -- -- 1.99 -- 41557 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)
2.63 2.72 97.7 0.448 -- 1.5 2.0 4136

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 2.63 47.506 -- 1.96 -- 41503 2114 97.86 -- 0.2349 0.2329 0.2728 --
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 2.63 2.6912 -- 148 2556 0.4282 0.4593 -- 97.0
X Ray Diffraction 2.6912 2.7585 -- 149 2664 0.3971 0.4335 -- 97.0
X Ray Diffraction 2.7585 2.8331 -- 126 2620 0.3664 0.3963 -- 98.0
X Ray Diffraction 2.8331 2.9164 -- 134 2626 0.3457 0.3848 -- 98.0
X Ray Diffraction 2.9164 3.0105 -- 141 2628 0.3349 0.4118 -- 98.0
X Ray Diffraction 3.0105 3.1181 -- 147 2606 0.3308 0.4383 -- 98.0
X Ray Diffraction 3.1181 3.2429 -- 144 2637 0.3083 0.3502 -- 98.0
X Ray Diffraction 3.2429 3.3905 -- 132 2657 0.2912 0.378 -- 98.0
X Ray Diffraction 3.3905 3.5692 -- 129 2655 0.2836 0.3175 -- 98.0
X Ray Diffraction 3.5692 3.7927 -- 146 2611 0.2453 0.3173 -- 98.0
X Ray Diffraction 3.7927 4.0854 -- 153 2614 0.21 0.2473 -- 98.0
X Ray Diffraction 4.0854 4.4962 -- 136 2694 0.1796 0.2106 -- 99.0
X Ray Diffraction 4.4962 5.1462 -- 160 2609 0.186 0.2291 -- 99.0
X Ray Diffraction 5.1462 6.481 -- 140 2637 0.1995 0.2258 -- 98.0
X Ray Diffraction 6.481 47.5133 -- 129 2575 0.2112 0.2251 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 92.7315
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.173
f_plane_restr 0.007
f_chiral_restr 0.054
f_angle_d 1.287
f_bond_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7406
Nucleic Acid Atoms 980
Heterogen Atoms 10
Solvent Atoms 44

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: 9.9.8.0L data reduction
D*trek data collection