4ERL

Crystal structure of the lysine riboswitch bound to a lysine-glycine dipeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D0UPDB ENTRY 3D0U)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP730310 mM Na-HEPES pH 7.0, 2 M Li2SO4, and 5 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties
Matthews coefficientSolvent content
4.6473.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.878α = 90
b = 119.878β = 90
c = 58.743γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 3152010-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
1319.6297.80.1130.1135.11.92188471.97247.24
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)
133.1196.50.3210.3211.91.931853

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3D0U)319.621.971868796599.160.19740.19530.2338RANDOM
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]
2.59352.593510.4317
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.848
f_angle_d0.933
f_chiral_restr0.06
f_plane_restr0.008
f_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms3479
Solvent Atoms10
Heterogen Atoms14

Software

Software
Software NamePurpose
CrystalCleardata collection
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling