4V9B

Crystal Structure of the 70S ribosome with tigecycline.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UZ6PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9
experimental modelPDB 3UZ7PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9
experimental modelPDB 3UZ8PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9
experimental modelPDB 3UZ9PDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52934% PEG20K, 4% PEGMME 550, 100mM Tris/HAc, 200mM KSCN, pH 7.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.362.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 210.06α = 90
b = 450.27β = 90
c = 616.89γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-02-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.000SLSX06SA

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
13.130099.90.46610.4644.510459461045188-3-396.184

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3UZ6, 3UZ7, 3UZ8, 3UZ93.1153.5881.3410459461045138200099.920.21360.21360.21350.2688RANDOM122.9958
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]
-14.39583.180511.2153
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.345
f_angle_d1.015
f_chiral_restr0.07
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19203
Nucleic Acid Atoms35778
Solvent Atoms
Heterogen Atoms966

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
RemDAqdata collection
PHENIXmodel building
XDSdata reduction
PHENIXphasing