3DIM

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Cs+ Soak


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% PEG4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6954.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.249α = 90
b = 79.043β = 90
c = 141.978γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.84APS24-ID-C

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
12.920970.1154.51411913695
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)
12.9396.80.2692.741401

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 3DIL2.920133691278868095.650.205250.205250.203080.24778RANDOM32.688
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]
0.7-3.462.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.326
r_angle_refined_deg1.293
r_scangle_it0.939
r_scbond_it0.59
r_mcangle_it0.387
r_nbtor_refined0.269
r_mcbond_it0.217
r_symmetry_hbond_refined0.2
r_nbd_refined0.172
r_xyhbond_nbd_refined0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.326
r_angle_refined_deg1.293
r_scangle_it0.939
r_scbond_it0.59
r_mcangle_it0.387
r_nbtor_refined0.269
r_mcbond_it0.217
r_symmetry_hbond_refined0.2
r_nbd_refined0.172
r_xyhbond_nbd_refined0.14
r_symmetry_vdw_refined0.133
r_chiral_restr0.065
r_metal_ion_refined0.058
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 Atoms26
Heterogen Atoms34

Software

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