6BZ6

Thermus thermophilus 70S complex containing 16S G347U ram mutation and empty A site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V97 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72934.8% PEG 20k, 4.8% PEG 550MME, 100 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8 mM DOBC
2VAPOR DIFFUSION, SITTING DROP72934.9% PEG 20k, 4.9% PEG 550MME, 100 mM TRIS-ACETATE, 200 mM KSCN, 10 mM MAGNESIUM ACETATE 2.8 mM DOBC
Crystal Properties
Matthews coefficientSolvent content
3.3162.82
3.3162.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.654α = 90
b = 447.955β = 90
c = 618.805γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-FS/N 60-0112-F2014-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.972APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.18124.48199.30.3040.3260.9957.977.76495876676.72
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.183.2699.32.152.3130.241.037.464

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4V973.18124.4811.339587234465899.290.23240.23160.251104.3743
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.039
f_angle_d0.99
f_chiral_restr0.054
f_plane_restr0.023
f_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms92857
Nucleic Acid Atoms197542
Solvent Atoms
Heterogen Atoms1372

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction