2HHH

Crystal structure of kasugamycin bound to the 30S ribosomal subunit


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5300MPD, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MES-KOH, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
4.6473.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 410.44α = 90
b = 410.44β = 90
c = 172.65γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.3598.498.47.720594420594429.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.353.4791.81.7

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 REPLACEMENTTHROUGHOUTEMPTY 30S3.3529.742059442059441020598.40.2680.2680.2650.289RANDOM40
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]
13.4213.42-26.84
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_improper_angle_d1.54
c_angle_deg1.4
c_bond_d0.01
c_dihedral_angle_d_prot
c_angle_d_na
c_angle_d
c_angle_deg_na
c_angle_deg_prot
c_bond_d_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_improper_angle_d1.54
c_angle_deg1.4
c_bond_d0.01
c_dihedral_angle_d_prot
c_angle_d_na
c_angle_d
c_angle_deg_na
c_angle_deg_prot
c_bond_d_na
c_dihedral_angle_d_na
c_angle_d_prot
c_bond_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19231
Nucleic Acid Atoms32349
Solvent Atoms
Heterogen Atoms52

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing