X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 291.0
Details 0.8-1.0 M lithium sulfate, 0.075-0.2 M potassium iodide, 0.05-0.2 M trisodium citrate, pH 5-6

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.97 α = 90
b = 135.97 β = 90
c = 181.57 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2014-11-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID

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
2.5 98.8 99.6 0.063 -- -- 4.4 -- 65579 -- -- 48.74
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)
2.497 2.51 -- -- -- -- -- --

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 2.497 58.878 -- 1.35 -- 65534 3249 99.5 -- 0.1881 0.1867 0.2151 --
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 2.4972 2.5345 -- 138 2750 0.2605 0.3 0.0 100.0
X Ray Diffraction 2.5345 2.5741 -- 150 2699 0.2577 0.314 0.0 100.0
X Ray Diffraction 2.5741 2.6163 -- 166 2694 0.252 0.2726 0.0 100.0
X Ray Diffraction 2.6163 2.6614 -- 166 2678 0.2482 0.2856 0.0 100.0
X Ray Diffraction 2.6614 2.7098 -- 136 2709 0.235 0.2369 0.0 100.0
X Ray Diffraction 2.7098 2.7619 -- 129 2711 0.2251 0.2686 0.0 100.0
X Ray Diffraction 2.7619 2.8183 -- 147 2702 0.2247 0.2529 0.0 100.0
X Ray Diffraction 2.8183 2.8796 -- 122 2722 0.23 0.2435 0.0 100.0
X Ray Diffraction 2.8796 2.9466 -- 141 2728 0.2308 0.2693 0.0 100.0
X Ray Diffraction 2.9466 3.0202 -- 123 2741 0.2431 0.2693 0.0 100.0
X Ray Diffraction 3.0202 3.1019 -- 154 2693 0.2324 0.2728 0.0 100.0
X Ray Diffraction 3.1019 3.1932 -- 150 2674 0.2252 0.2465 0.0 100.0
X Ray Diffraction 3.1932 3.2962 -- 139 2734 0.2139 0.2642 0.0 100.0
X Ray Diffraction 3.2962 3.414 -- 133 2703 0.2178 0.2495 0.0 100.0
X Ray Diffraction 3.414 3.5507 -- 127 2715 0.2068 0.2486 0.0 100.0
X Ray Diffraction 3.5507 3.7123 -- 158 2693 0.1961 0.2434 0.0 99.0
X Ray Diffraction 3.7123 3.908 -- 131 2721 0.1758 0.2155 0.0 100.0
X Ray Diffraction 3.908 4.1527 -- 115 2712 0.151 0.1638 0.0 99.0
X Ray Diffraction 4.1527 4.4733 -- 153 2687 0.1488 0.161 0.0 99.0
X Ray Diffraction 4.4733 4.9232 -- 138 2709 0.1404 0.1653 0.0 99.0
X Ray Diffraction 4.9232 5.6351 -- 113 2745 0.1532 0.1822 0.0 99.0
X Ray Diffraction 5.6351 7.0978 -- 182 2663 0.1789 0.1939 0.0 99.0
X Ray Diffraction 7.0978 58.8939 -- 138 2702 0.1543 0.1777 0.0 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.0815
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.323
f_bond_d 0.005
f_chiral_restr 0.041
f_plane_restr 0.003
f_angle_d 0.585
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8936
Nucleic Acid Atoms 0
Heterogen Atoms 313
Solvent Atoms 218

Software

Software
Software Name Purpose
Aimless data scaling
PHENIX refinement version: 1.10_2155
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHASER phasing