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 (Hampton Research), pH 8.5-9.0, 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 prior to freezing, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.65 α = 101.08
b = 63.87 β = 106.22
c = 105.1 γ = 103.03
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
2.85 45.69 98.3 0.047 -- -- 2.01 -- 34198 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)
2.85 2.95 98.1 0.442 -- 1.8 2.02 3403

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 43.263 -- 1.97 -- 34099 1743 98.05 -- 0.2216 0.2186 0.2757 --
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 2.9338 -- 150 2692 0.3582 0.3788 -- 98.0
X Ray Diffraction 2.9338 3.0285 -- 144 2701 0.3233 0.3775 -- 98.0
X Ray Diffraction 3.0285 3.1367 -- 145 2644 0.2982 0.3778 -- 98.0
X Ray Diffraction 3.1367 3.2623 -- 136 2699 0.2815 0.3164 -- 98.0
X Ray Diffraction 3.2623 3.4107 -- 140 2742 0.2778 0.3807 -- 98.0
X Ray Diffraction 3.4107 3.5904 -- 139 2713 0.2803 0.3532 -- 98.0
X Ray Diffraction 3.5904 3.8153 -- 149 2688 0.2934 0.3945 -- 98.0
X Ray Diffraction 3.8153 4.1096 -- 147 2659 0.2134 0.276 -- 98.0
X Ray Diffraction 4.1096 4.5228 -- 145 2754 0.1753 0.2195 -- 98.0
X Ray Diffraction 4.5228 5.1763 -- 146 2688 0.1697 0.2394 -- 98.0
X Ray Diffraction 5.1763 6.5181 -- 161 2723 0.1925 0.2726 -- 99.0
X Ray Diffraction 6.5181 43.2675 -- 141 2653 0.1925 0.2112 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 96.6887
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.781
f_plane_restr 0.007
f_chiral_restr 0.049
f_angle_d 1.253
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7406
Nucleic Acid Atoms 1544
Heterogen Atoms 20
Solvent Atoms 57

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: 9.9.9.4D data reduction
D*trek data collection