2GDI

Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.929328 % PEG4000, 100 mM Na-acetate, pH 4.8, and 200 mM NH4-acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.90
Crystal Properties
Matthew coefficientSolvent content
238.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.819α = 90
b = 29.558β = 94.55
c = 95.17γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-11-07MSINGLE WAVELENGTH
21x-rayCCDADSC QUANTUM 3152005-11-07MMAD
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25
2SYNCHROTRONNSLS BEAMLINE X251.1407, 1.1411, 1.1201NSLSX25

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
1,22.052099.80.0624.327007
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)
1,22.052.121000.4752.894.3

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.05202530925258133799.80.210.2080.241RANDOM34.95
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]
-0.76-2.371.81-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.196
r_angle_refined_deg1.043
r_scbond_it0.85
r_mcangle_it0.435
r_nbtor_refined0.284
r_mcbond_it0.199
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.177
r_nbd_refined0.164
r_symmetry_vdw_refined0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.196
r_angle_refined_deg1.043
r_scbond_it0.85
r_mcangle_it0.435
r_nbtor_refined0.284
r_mcbond_it0.199
r_xyhbond_nbd_refined0.191
r_symmetry_hbond_refined0.177
r_nbd_refined0.164
r_symmetry_vdw_refined0.16
r_metal_ion_refined0.141
r_chiral_restr0.129
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_nbtor_other
r_dihedral_angle_3_deg
r_bond_other_d
r_dihedral_angle_4_deg
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_angle_other_deg
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_gen_planes_other
r_mcbond_other
r_dihedral_angle_1_deg
r_nbd_other
r_dihedral_angle_2_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 Atoms3442
Solvent Atoms312
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
CAD4data reduction
HKL-2000data scaling
SOLVEphasing