3DIZ

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine in the Absence of Mg2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DILpdb entry 3DIL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.729318% PEG 4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54α = 90
b = 78.803β = 90
c = 140.631γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2008-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.8520870.10515.73.81534413349
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)
12.852.9589.20.4982.73.91489

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 3DIL2.8520138261204863987.140.195480.195480.192780.24388RANDOM45.32
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]
-3.43-4.68.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.992
r_angle_refined_deg1.328
r_scangle_it0.869
r_scbond_it0.555
r_mcangle_it0.406
r_nbtor_refined0.27
r_mcbond_it0.207
r_symmetry_hbond_refined0.187
r_nbd_refined0.172
r_symmetry_vdw_refined0.156
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.992
r_angle_refined_deg1.328
r_scangle_it0.869
r_scbond_it0.555
r_mcangle_it0.406
r_nbtor_refined0.27
r_mcbond_it0.207
r_symmetry_hbond_refined0.187
r_nbd_refined0.172
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_refined0.154
r_chiral_restr0.066
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms3752
Solvent Atoms10
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing