3DJ0

Crystallization of the Thermotoga maritima lysine riboswitch bound to L-4-oxalysine


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
2.7154.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.541α = 90
b = 79.095β = 90
c = 142.535γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.24APS24-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
12.52097.70.08527.862222821717
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)
12.52.5995.20.4974.35.92170

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 3DIL2.5202086820432109597.910.214230.214230.211510.26788RANDOM32.023
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]
-1.57-4.245.81
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.254
r_scangle_it0.946
r_scbond_it0.638
r_mcangle_it0.276
r_nbtor_refined0.265
r_mcbond_it0.262
r_nbd_refined0.163
r_metal_ion_refined0.153
r_symmetry_vdw_refined0.153
r_symmetry_hbond_refined0.151
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.254
r_scangle_it0.946
r_scbond_it0.638
r_mcangle_it0.276
r_nbtor_refined0.265
r_mcbond_it0.262
r_nbd_refined0.163
r_metal_ion_refined0.153
r_symmetry_vdw_refined0.153
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.126
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms3752
Solvent Atoms83
Heterogen Atoms28

Software

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