3DIX

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, K+ anomalous data


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
2.6453.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.108α = 90
b = 78.902β = 90
c = 140.167γ = 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
12.92097.50.11812.44.31387013523
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)
12.9397.30.3312.53.61325

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 3DIL2.920131421282167097.560.172780.172780.17110.20525RANDOM34.281
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]
0.09-1.361.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.531
r_angle_refined_deg1.259
r_scangle_it0.997
r_scbond_it0.614
r_nbtor_refined0.266
r_mcangle_it0.245
r_mcbond_it0.161
r_symmetry_vdw_refined0.16
r_nbd_refined0.159
r_symmetry_hbond_refined0.151
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg10.531
r_angle_refined_deg1.259
r_scangle_it0.997
r_scbond_it0.614
r_nbtor_refined0.266
r_mcangle_it0.245
r_mcbond_it0.161
r_symmetry_vdw_refined0.16
r_nbd_refined0.159
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.109
r_chiral_restr0.055
r_metal_ion_refined0.031
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 Atoms18
Heterogen Atoms16

Software

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