1N8R

Structure of large ribosomal subunit in complex with virginiamycin M


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.82921.2M KCl, 0.5M (NH4)Cl, 30mM MgCl2, 8% PEG, pH 5.80, VAPOR DIFFUSION, SITTING DROP at 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-ray100CCDMARRESEARCH2000-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.0332NSLSX25

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
135098.70.1440.1447.73.6344322339727-333.1
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)
33.0597.70.490.491.72.116729

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JJ2320346861327972320394.60.20110.2010.242same reflections as 1JJ243.9
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]
5.141.7-6.84
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d15.6
c_scangle_it2.02
c_mcangle_it1.84
c_improper_angle_d1.57
c_angle_deg1.3
c_scbond_it1.3
c_mcbond_it1.12
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28801
Nucleic Acid Atoms61617
Solvent Atoms7882
Heterogen Atoms269

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing