3OXJ

crystal structure of glycine riboswitch, soaked in Ba2+


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.1293.150.05 M Na-cacodylate, pH 5.1, 0.2 M KCl, 8 % (w/v) PEG8000 and 80 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties
Matthew coefficientSolvent content
3.5965.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.215α = 90
b = 84.215β = 90
c = 201.382γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.5000NSLSX29A

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
13.22099.90.0829.25.21423014230-3-3
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)
3.23.311000.543.15.41390

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT3.220134971348271499.890.19590.19590.194450.22421RANDOM102.162
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.11
r_scangle_it0.962
r_scbond_it0.552
r_mcangle_it0.172
r_mcbond_it0.092
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_sphericity_bonded
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_angle_refined_deg1.11
r_scangle_it0.962
r_scbond_it0.552
r_mcangle_it0.172
r_mcbond_it0.092
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_sphericity_bonded
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_dihedral_angle_1_deg
r_mcbond_other
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms3790
Solvent Atoms38
Heterogen Atoms55

Software

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