3DIQ

Crystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine


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
2.6253.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.746α = 90
b = 78.794β = 90
c = 140.069γ = 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-E0.9795APS24-ID-E

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
12.72094.90.11913.24.71704116172
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)
2.72.8890.562.44.51662

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 DIFFRACTIONREFMACTHROUGHOUTpdb entry 3DIL2.720160811526180694.90.203840.203840.201820.24134RANDOM24.898
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]
-1.03-0.631.66
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.181
r_scangle_it1.165
r_scbond_it0.727
r_nbtor_refined0.266
r_mcangle_it0.261
r_nbd_refined0.154
r_symmetry_hbond_refined0.15
r_symmetry_vdw_refined0.131
r_xyhbond_nbd_refined0.13
r_mcbond_it0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.181
r_scangle_it1.165
r_scbond_it0.727
r_nbtor_refined0.266
r_mcangle_it0.261
r_nbd_refined0.154
r_symmetry_hbond_refined0.15
r_symmetry_vdw_refined0.131
r_xyhbond_nbd_refined0.13
r_mcbond_it0.116
r_chiral_restr0.062
r_metal_ion_refined0.038
r_bond_refined_d0.005
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms3752
Solvent Atoms43
Heterogen Atoms27

Software

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