3DIY

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, Mn2+ 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% PEG 4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.193α = 90
b = 78.662β = 90
c = 140.522γ = 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
12.72096.60.09521.85.91696916392
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)
12.72.895.90.5882.85.61658

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 3DIL2.7120161071551082296.290.190990.190990.188720.23671RANDOM35.039
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]
0.2-1.911.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg8.221
r_angle_refined_deg1.239
r_scangle_it1.045
r_scbond_it0.666
r_mcangle_it0.312
r_nbtor_refined0.265
r_symmetry_hbond_refined0.171
r_nbd_refined0.155
r_metal_ion_refined0.147
r_xyhbond_nbd_refined0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg8.221
r_angle_refined_deg1.239
r_scangle_it1.045
r_scbond_it0.666
r_mcangle_it0.312
r_nbtor_refined0.265
r_symmetry_hbond_refined0.171
r_nbd_refined0.155
r_metal_ion_refined0.147
r_xyhbond_nbd_refined0.134
r_symmetry_vdw_refined0.126
r_mcbond_it0.123
r_chiral_restr0.051
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms3756
Solvent Atoms37
Heterogen Atoms21

Software

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