X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 277.15
Details This RNA was prepared for crystallography in a solution containing 5 mg/mL RNA, 2.5 mM MgCl2, and 10 mM HEPES-KOH pH 7.5. This mixture was heated to 65?C for 3 minutes, then cooled at room temperature. After cooling, Spermidine was added to 0.5 mM. The reaction was centrifuged for 10 minutes at 13000 x g and then used in sitting-drop vapor diffusion crystallization at 4?C. 1 ?L of RNA solution was combined with 2 ?L of 10% MPD, 40 mM Na-Cacodylate pH 6.0, 12 mM Spermine, 80 mM NaCl, and 20 mM MgCl2. The well solution was 20-35% MPD. Crystals appeared and grew to full size over the course of 1-2 days.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.27 α = 90
b = 101.57 β = 90
c = 111.61 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CMOS RDI CMOS_8M -- 2013-10-21
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock Si(111) sagitally focused monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 4.2.2 1.0972 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
1.99 66 99.4 0.054 -- -- 7.45 -- 41343 -- 2.0 --
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)
1.99 2.03 94.7 0.82 -- 2.19 -- --

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
SAD 1.9912 28.871 -- 1.34 -- 41334 3790 99.46 -- 0.2088 0.2057 0.2396 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 1.9912 2.0164 -- 126 1239 0.3046 0.3259 -- 90.0
X Ray Diffraction 2.0164 2.043 -- 139 1395 0.2973 0.3908 -- 100.0
X Ray Diffraction 2.043 2.0709 -- 148 1410 0.2883 0.3024 -- 100.0
X Ray Diffraction 2.0709 2.1005 -- 136 1379 0.283 0.323 -- 100.0
X Ray Diffraction 2.1005 2.1319 -- 140 1391 0.2746 0.2785 -- 100.0
X Ray Diffraction 2.1319 2.1652 -- 140 1396 0.2567 0.2982 -- 100.0
X Ray Diffraction 2.1652 2.2007 -- 139 1388 0.236 0.2496 -- 100.0
X Ray Diffraction 2.2007 2.2386 -- 143 1410 0.2346 0.2812 -- 100.0
X Ray Diffraction 2.2386 2.2793 -- 143 1401 0.2277 0.2925 -- 100.0
X Ray Diffraction 2.2793 2.3231 -- 138 1363 0.2262 0.2641 -- 100.0
X Ray Diffraction 2.3231 2.3705 -- 143 1413 0.2316 0.2825 -- 100.0
X Ray Diffraction 2.3705 2.422 -- 142 1419 0.2279 0.277 -- 100.0
X Ray Diffraction 2.422 2.4783 -- 141 1377 0.2295 0.2489 -- 100.0
X Ray Diffraction 2.4783 2.5403 -- 143 1396 0.2501 0.3312 -- 100.0
X Ray Diffraction 2.5403 2.6089 -- 142 1396 0.2497 0.2752 -- 100.0
X Ray Diffraction 2.6089 2.6856 -- 143 1404 0.2521 0.2989 -- 100.0
X Ray Diffraction 2.6856 2.7722 -- 147 1400 0.2557 0.285 -- 100.0
X Ray Diffraction 2.7722 2.8712 -- 142 1395 0.2741 0.2994 -- 100.0
X Ray Diffraction 2.8712 2.9861 -- 133 1391 0.2373 0.3721 -- 100.0
X Ray Diffraction 2.9861 3.1218 -- 143 1404 0.2053 0.2124 -- 100.0
X Ray Diffraction 3.1218 3.2862 -- 136 1403 0.1825 0.2412 -- 100.0
X Ray Diffraction 3.2862 3.4918 -- 141 1413 0.1804 0.2382 -- 100.0
X Ray Diffraction 3.4918 3.7608 -- 139 1369 0.1743 0.1896 -- 100.0
X Ray Diffraction 3.7608 4.1383 -- 143 1421 0.1764 0.205 -- 100.0
X Ray Diffraction 4.1383 4.7349 -- 144 1387 0.1695 0.1714 -- 100.0
X Ray Diffraction 4.7349 5.9568 -- 138 1392 0.1556 0.2057 -- 100.0
X Ray Diffraction 5.9568 28.8736 -- 138 1392 0.2029 0.2058 -- 98.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.011
f_plane_restr 0.013
f_angle_d 1.791
f_chiral_restr 0.082
f_dihedral_angle_d 14.148
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers

Software

Software
Software Name Purpose
PHENIX refinement version: (phenix.refine: 1.8.4_1496)