1K9M

Co-crystal structure of tylosin bound to the 50S ribosomal subunit of Haloarcula marismortui


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JJ2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.8292PEG 6K, KCl, Na-acetate, NH4Cl, MgCl2, pH 5.8, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
3.1761.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 212.902α = 90
b = 300.474β = 90
c = 575.176γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2000-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.033APS19-ID

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
13200.150.1512.86366365366365-3-339.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
33.1195.20.7090.7092.3434695

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1JJ2319.99359798337448330392.90.2190.2190.2190.262RANDOM same as 1JJ255.1
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]
12.15-5.96-6.2
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.7
c_scangle_it1.99
c_mcangle_it1.81
c_improper_angle_d1.6
c_angle_deg1.3
c_scbond_it1.24
c_mcbond_it1.05
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.7
c_scangle_it1.99
c_mcangle_it1.81
c_improper_angle_d1.6
c_angle_deg1.3
c_scbond_it1.24
c_mcbond_it1.05
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28801
Nucleic Acid Atoms61617
Solvent Atoms7877
Heterogen Atoms298

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing