5J8A

Structure of the E coli 70S ribosome with the U1052G mutation in 16S rRNA bound to tigecycline


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH291PEG 8k, Spermidine, Putrescine, Ammonium Chloride, MAgnesium Chloride, MPD, MES pH 6.5
Crystal Properties
Matthews coefficientSolvent content
3.3863.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 211.72α = 90
b = 435.19β = 90
c = 622.83γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1APS17-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.148.5399.712.861027314

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT3.148.531025393408799.70.1710.1710.192RANDOM112.85
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]
1.337213.1149-14.4521
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.54
t_omega_torsion2.33
t_angle_deg0.82
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion21.54
t_omega_torsion2.33
t_angle_deg0.82
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms90649
Nucleic Acid Atoms195380
Solvent Atoms7744
Heterogen Atoms1176

Software

Software
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing