X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 1.25 M lithium sulfate, 0.5 M ammonium sulfate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.46 α = 90
b = 66.87 β = 93.31
c = 65.13 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-12-08
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 1.12 ALS 12.3.1

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
1.65 50 99.5 0.035 -- -- 5.0 39245 39245 0.0 -3.0 --
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)
1.65 1.69 99.7 0.645 -- 2.3 5.0 2902

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 1.65 39.072 -- 1.34 -- 39243 1934 99.41 -- 0.1928 0.191 0.2282 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 1.65 1.6913 -- 164 2640 0.294 0.3409 -- 100.0
X Ray Diffraction 1.6913 1.737 -- 125 2639 0.2746 0.3605 -- 100.0
X Ray Diffraction 1.737 1.7881 -- 134 2664 0.2556 0.2556 -- 100.0
X Ray Diffraction 1.7881 1.8458 -- 125 2666 0.244 0.28 -- 100.0
X Ray Diffraction 1.8458 1.9118 -- 140 2698 0.2218 0.2731 -- 100.0
X Ray Diffraction 1.9118 1.9883 -- 154 2622 0.2132 0.2676 -- 99.0
X Ray Diffraction 1.9883 2.0788 -- 133 2663 0.1915 0.2352 -- 100.0
X Ray Diffraction 2.0788 2.1884 -- 126 2698 0.1769 0.211 -- 100.0
X Ray Diffraction 2.1884 2.3255 -- 156 2655 0.1826 0.2366 -- 100.0
X Ray Diffraction 2.3255 2.5051 -- 148 2643 0.1802 0.221 -- 100.0
X Ray Diffraction 2.5051 2.7571 -- 128 2693 0.1802 0.2276 -- 100.0
X Ray Diffraction 2.7571 3.1559 -- 120 2714 0.1836 0.218 -- 100.0
X Ray Diffraction 3.1559 3.9755 -- 139 2697 0.1696 0.2382 -- 100.0
X Ray Diffraction 3.9755 39.0825 -- 142 2617 0.1945 0.1935 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.8603
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.7342
Anisotropic B[2][2] 1.6059
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.7455
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.072
f_dihedral_angle_d 13.243
f_angle_d 1.264
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1859
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 208

Software

Computing
Computing Package Purpose
Blue Ice Data Collection
XDS (xia2) Data Reduction (intensity integration)
XDS (xia2, scala) Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHASER model building
Blue version: Ice data collection