X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SDSM. jannaschii L7Ae protein (PDB ID 1SDS, chain A)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6294.15150 M RNA, 210 M YbxF, 10 mM MgCl2, 10 mM SAM, 40 mM KCl, 20 mM HEPES-KOH, 1 mM spermine, 1 mM cobalt hexammine, and 1 mM DTT, 100 mM potassium cacodylate pH 6.0, 200 mM MgCl2 and 25% (v/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K
Crystal Properties
Matthews coefficientSolvent content
2.5251.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 191.762α = 90
b = 54.305β = 116.56
c = 106.366γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21ALS5.0.2

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
12.8500.09825.24.32520222926116.2121.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.992.72.464.32244

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTM. jannaschii L7Ae protein (PDB ID 1SDS, chain A)2.829.5422926227693.40.2180.2180.274RANDOM75.6
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]
25.1215.887.19-32.32
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_scangle_it6.87
c_mcangle_it5.58
c_scbond_it4.99
c_mcbond_it3.52
c_improper_angle_d1.73
c_angle_deg1.4
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d18.5
c_scangle_it6.87
c_mcangle_it5.58
c_scbond_it4.99
c_mcbond_it3.52
c_improper_angle_d1.73
c_angle_deg1.4
c_bond_d0.006
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 Atoms962
Nucleic Acid Atoms5372
Solvent Atoms15
Heterogen Atoms202

Software

Software
Software NamePurpose
ALSdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling