1KD1

Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JJ21JJ2.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.8292PEG 6K, KCl, NH4Cl, NaOAc, 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-MADESi-111, Si-2202000-09-28MSINGLE 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
135099.90.1520.15212.17363802363802-3-342.9
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)
33.1199.90.8530.8532.6536147

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 REPLACEMENTTHROUGHOUT1JJ2.pdb319.99357528333395327891.70.220.220.220.269RANDOM IDENTICAL TEST set from 1JJ2.pdb58.7
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]
15.27-5.73-9.54
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.7
c_scangle_it1.93
c_mcangle_it1.76
c_improper_angle_d1.59
c_angle_deg1.4
c_scbond_it1.21
c_mcbond_it1.02
c_bond_d0.009
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d17.7
c_scangle_it1.93
c_mcangle_it1.76
c_improper_angle_d1.59
c_angle_deg1.4
c_scbond_it1.21
c_mcbond_it1.02
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 Atoms7876
Heterogen Atoms293

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing