X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 293.0
Details 100 mM MES, 100 mM Lithium Acetate, 15% (w/v) polyethylene glycol 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.04 α = 90
b = 101.08 β = 90
c = 115.45 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS EIGER X 16M -- 2015-06-15
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 0.99203 APS 22-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
2.05 50 99.7 0.1 -- -- 7.3 -- 53293 -- -- 33.93
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)
2.05 2.12 97.4 -- -- -- 6.5 --

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 2.052 36.02 -- 1.34 -- 53178 2673 99.54 -- 0.1717 0.17 0.2008 --
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 2.0524 2.0897 -- 131 2460 0.3202 0.3357 -- 94.0
X Ray Diffraction 2.0897 2.1299 -- 138 2622 0.2814 0.3172 -- 99.0
X Ray Diffraction 2.1299 2.1733 -- 140 2651 0.2334 0.2768 -- 100.0
X Ray Diffraction 2.1733 2.2206 -- 132 2632 0.2315 0.2841 -- 100.0
X Ray Diffraction 2.2206 2.2722 -- 118 2638 0.2222 0.2856 -- 100.0
X Ray Diffraction 2.2722 2.329 -- 117 2677 0.2026 0.2687 -- 100.0
X Ray Diffraction 2.329 2.392 -- 142 2648 0.1956 0.2571 -- 100.0
X Ray Diffraction 2.392 2.4624 -- 160 2611 0.1843 0.2263 -- 100.0
X Ray Diffraction 2.4624 2.5418 -- 153 2622 0.1856 0.2504 -- 100.0
X Ray Diffraction 2.5418 2.6327 -- 138 2662 0.1753 0.2279 -- 100.0
X Ray Diffraction 2.6327 2.738 -- 126 2682 0.1724 0.2145 -- 100.0
X Ray Diffraction 2.738 2.8626 -- 145 2631 0.1836 0.2069 -- 100.0
X Ray Diffraction 2.8626 3.0134 -- 148 2680 0.1858 0.222 -- 100.0
X Ray Diffraction 3.0134 3.2021 -- 142 2660 0.1837 0.22 -- 100.0
X Ray Diffraction 3.2021 3.4492 -- 140 2670 0.1597 0.2008 -- 99.0
X Ray Diffraction 3.4492 3.796 -- 145 2678 0.1544 0.161 -- 100.0
X Ray Diffraction 3.796 4.3444 -- 147 2696 0.1323 0.1624 -- 100.0
X Ray Diffraction 4.3444 5.4704 -- 168 2730 0.1279 0.1664 -- 100.0
X Ray Diffraction 5.4704 36.025 -- 143 2855 0.1595 0.1647 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_angle_d 0.804
f_bond_d 0.01
f_chiral_restr 0.047
f_dihedral_angle_d 18.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5022
Nucleic Acid Atoms 731
Heterogen Atoms 35
Solvent Atoms 562

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10.1_2155)
SCALEPACK data scaling
PDB_EXTRACT data extraction version: 3.25
PHENIX phasing
HKL-2000 data collection
HKL-2000 data reduction