2ZM6

Crystal structure of the Thermus thermophilus 30S ribosomal subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E5L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829810mM HEPES-KOH, 10mM MgCl2, 60mM NH4Cl, 6mM beta-mercaptoethanol, 11-12% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.874.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 411.5α = 90
b = 411.5β = 90
c = 172.58γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMAR CCD 225 mmDynamically bendable mirror2005-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.98000SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.220097.70.1465.723.1241354235783-383.224
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.23.397.20.6731.9320481

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2E5L3.3184.032153091094297.70.2920.323RANDOM109.3
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]
13.113.1-26.19
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d19.9
c_improper_angle_d1.84
c_angle_deg1.7
c_bond_d0.012
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18934
Nucleic Acid Atoms32372
Solvent Atoms
Heterogen Atoms2

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction