4V9D

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I1MPDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P
experimental modelPDB 3I1NPDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P
experimental modelPDB 3I1OPDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P
experimental modelPDB 3I1PPDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.5291PEG8000, MPD, pH 6.5, microbatch, temperature 291K
2MICROBATCH6.5291PEG8000, MPD, pH 6.5, microbatch, temperature 291K
3MICROBATCH6.5291PEG8000, MPD, pH 6.5, microbatch, temperature 291K
4MICROBATCH6.5291PEG8000, MPD, pH 6.5, microbatch, temperature 291K
5MICROBATCH6.5291PEG8000, MPD, pH 6.5, microbatch, temperature 291K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 211.67α = 90
b = 438.07β = 90
c = 613.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-12-03MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 3152010-10-16MSINGLE WAVELENGTH
31x-ray100CCDADSC QUANTUM 3152010-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1ALS8.3.1
2SYNCHROTRONALS BEAMLINE 12.3.11.1ALS12.3.1
3SYNCHROTRONAPS BEAMLINE 24-ID-C0.97APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
1,2,334083.50.1947.38938380-351.273
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,2,333.1643.50.8161.18

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISPDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P3401.8938304938304190210.2030.2020.26RANDOM41.6019
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19973
Nucleic Acid Atoms34942
Solvent Atoms203
Heterogen Atoms72

Software

Software
Software NamePurpose
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing