3PIP

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZJRPDB ENTRY 2ZJR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Crystal Properties
Matthews coefficientSolvent content
4.472.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.723α = 90
b = 408.562β = 90
c = 693.334γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
13.4519.99884.30.2160.0965.64.62601940.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.453.5785.61.44.5

Refinement

Statistics
Diffraction IDStructure Solution 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 DIFFRACTIONISOMORPHOUS REPLACEMENTPDB ENTRY 2ZJR3.4519.9980.58260194263583.30.2570.2570.301
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]
-20.5146.816-25.6717
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.358
f_angle_d1.271
f_chiral_restr0.067
f_bond_d0.013
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24479
Nucleic Acid Atoms59311
Solvent Atoms
Heterogen Atoms173

Software

Software
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing