4V7T

Crystal structure of the E. coli ribosome bound to chloramphenicol.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.5291PEG8k, MPD, pH 6.5, microbatch, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.3763.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 211.456α = 90
b = 434.084β = 90
c = 621.233γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.1158ALS8.3.1

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
13.19410082.60.07212.727033127087601.81.8
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)
13.1943.4269.70.4351.5

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-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISPDB ENTRY 3I1M, 3I1N, 3I1O, 3I1P3.194282.1460.067087607087601429875.810.19190.19060.252
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]
-2.331-7.60017.0078
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d28.169
f_angle_d1.427
f_chiral_restr0.077
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms89372
Nucleic Acid Atoms193031
Solvent Atoms1712
Heterogen Atoms384

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement
DENZOdata reduction