4YPB

Precleavage 70S structure of the P. vulgaris HigB DeltaH92 toxin bound to the AAA codon


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 4% PEG 20k, 4% PEG550 MME, 0.1M TRIS-ACETATE, 0.2M KSCN

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 214.11 α = 90
b = 453.88 β = 90
c = 607.59 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2012-07-29
CCD ADSC QUANTUM 315 -- 2012-08-05
Diffraction Radiation
Monochromator Protocol
Kohzu HLD8-24 monochromator SINGLE WAVELENGTH
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
SYNCHROTRON APS BEAMLINE 24-ID-E 0.97921 APS 24-ID-E

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
3.4 35 98.9 0.213 -- -- 6.0 -- 794344 -- -3.0 81.44
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)
3.4 3.5 99.6 1.047 -- 1.75 6.0 --

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 3.4 34.932 -- 1.36 -- 794344 49419 99.32 -- 0.2035 0.202 0.2344 inherited from 2J00, 2J01, 2J02, 2J03
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 3.4 3.4386 -- 1328 25171 0.3016 0.3308 -- 100.0
X Ray Diffraction 3.4386 3.479 -- 1257 25190 0.2894 0.3176 -- 100.0
X Ray Diffraction 3.479 3.5214 -- 1287 25199 0.289 0.3185 -- 100.0
X Ray Diffraction 3.5214 3.5659 -- 1327 25206 0.2811 0.3065 -- 100.0
X Ray Diffraction 3.5659 3.6128 -- 1298 25038 0.2733 0.3042 -- 99.0
X Ray Diffraction 3.6128 3.6623 -- 1304 24992 0.2681 0.2898 -- 99.0
X Ray Diffraction 3.6623 3.7145 -- 1266 24677 0.2565 0.2799 -- 98.0
X Ray Diffraction 3.7145 3.7699 -- 1282 25241 0.2483 0.2924 -- 100.0
X Ray Diffraction 3.7699 3.8287 -- 1355 25223 0.2429 0.2644 -- 100.0
X Ray Diffraction 3.8287 3.8914 -- 1291 25324 0.2328 0.2697 -- 100.0
X Ray Diffraction 3.8914 3.9584 -- 1297 25230 0.2322 0.2633 -- 100.0
X Ray Diffraction 3.9584 4.0303 -- 1313 25204 0.2245 0.2636 -- 100.0
X Ray Diffraction 4.0303 4.1077 -- 1319 25277 0.2209 0.2548 -- 100.0
X Ray Diffraction 4.1077 4.1914 -- 1318 25219 0.2167 0.2519 -- 100.0
X Ray Diffraction 4.1914 4.2824 -- 1361 25198 0.2101 0.2537 -- 100.0
X Ray Diffraction 4.2824 4.3819 -- 1229 25203 0.207 0.2355 -- 99.0
X Ray Diffraction 4.3819 4.4912 -- 968 25450 0.2061 0.2264 -- 99.0
X Ray Diffraction 4.4912 4.6124 -- 716 25289 0.195 0.2418 -- 98.0
X Ray Diffraction 4.6124 4.7478 -- 910 25715 0.1993 0.2384 -- 100.0
X Ray Diffraction 4.7478 4.9007 -- 1083 25473 0.1894 0.1998 -- 99.0
X Ray Diffraction 4.9007 5.0753 -- 1273 25333 0.19 0.226 -- 99.0
X Ray Diffraction 5.0753 5.2779 -- 1336 25237 0.1819 0.221 -- 99.0
X Ray Diffraction 5.2779 5.5172 -- 1322 25169 0.1803 0.2145 -- 99.0
X Ray Diffraction 5.5172 5.8068 -- 1268 25155 0.1834 0.2198 -- 98.0
X Ray Diffraction 5.8068 6.1688 -- 1297 24768 0.1873 0.2297 -- 97.0
X Ray Diffraction 6.1688 6.6421 -- 1322 25274 0.1893 0.2367 -- 99.0
X Ray Diffraction 6.6421 7.305 -- 1041 25508 0.1863 0.2413 -- 98.0
X Ray Diffraction 7.305 8.3495 -- 850 25564 0.1953 0.2338 -- 98.0
X Ray Diffraction 8.3495 10.4725 -- 1040 25224 0.2158 0.2447 -- 96.0
X Ray Diffraction 10.4725 34.9929 -- 1229 25358 0.2102 0.2183 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 76.74
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.049
f_angle_d 0.836
f_bond_d 0.005
f_dihedral_angle_d 16.935
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 94471
Nucleic Acid Atoms 201748
Heterogen Atoms 1312
Solvent Atoms 0

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
PDB_EXTRACT data extraction version: 3.14
PHENIX phasing