3DIS

Crystallization of the Thermotoga maritima lysine riboswitch in free form


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
2.6753.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.252α = 90
b = 78.624β = 90
c = 141.876γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS2008-05-12MSINGLE 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
13.12092.80.1977.54.31146910643
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)
13.13.289.50.4992.84.31124

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 REPLACEMENTTHROUGHOUTpdb entry 3DIL3.120109171009851692.50.18960.18960.187730.22764RANDOM39.715
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]
-2.94-3.86.74
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.228
r_scangle_it0.819
r_scbond_it0.472
r_nbtor_refined0.27
r_symmetry_hbond_refined0.184
r_symmetry_vdw_refined0.164
r_nbd_refined0.158
r_xyhbond_nbd_refined0.146
r_mcbond_it0.099
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.228
r_scangle_it0.819
r_scbond_it0.472
r_nbtor_refined0.27
r_symmetry_hbond_refined0.184
r_symmetry_vdw_refined0.164
r_nbd_refined0.158
r_xyhbond_nbd_refined0.146
r_mcbond_it0.099
r_chiral_restr0.068
r_metal_ion_refined0.04
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 Atoms6
Heterogen Atoms14

Software

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