3SKT

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'- Deoxyguanosine, manganese Soak


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.05 M Na-HEPES, pH 7.5, ~40 % (v/v) pentaerythritol propoxylate, 0.2 M KCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.031α = 90
b = 34.632β = 92.81
c = 111.598γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.5NSLSX29A

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
13.12097.90.13619.95.970696921
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)
13.13.2185.20.246.64.5586

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMolrepTHROUGHOUT3.120653231798.120.198670.196070.252RANDOM64.159
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]
-4.68-7.95-3.667.57
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.186
r_angle_refined_deg1.132
r_scbond_it0.702
r_nbtor_refined0.283
r_nbd_refined0.186
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.171
r_symmetry_vdw_refined0.141
r_chiral_restr0.057
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.186
r_angle_refined_deg1.132
r_scbond_it0.702
r_nbtor_refined0.283
r_nbd_refined0.186
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.171
r_symmetry_vdw_refined0.141
r_chiral_restr0.057
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_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2826
Solvent Atoms10
Heterogen Atoms57

Software

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