3F4E

Crystal structure of the FMN riboswitch bound to FMN, split RNA.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F2Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 MES-Na pH 6.5 10% PEG 4000 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9257.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.471α = 90
b = 71.471β = 90
c = 140.554γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.08NSLSX29A

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
13.052099.30.06160.716.483378297
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)
13.053.1698.60.5118.215.8813

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 REPLACEMENTTHROUGHOUT3F2Q3.05207953786938298.940.201050.201050.199550.23176RANDOM63.051
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]
2.691.342.69-4.03
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.472
r_angle_refined_deg1.028
r_scbond_it0.886
r_nbtor_refined0.281
r_xyhbond_nbd_refined0.173
r_nbd_refined0.172
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.142
r_metal_ion_refined0.074
r_chiral_restr0.053
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.472
r_angle_refined_deg1.028
r_scbond_it0.886
r_nbtor_refined0.281
r_xyhbond_nbd_refined0.173
r_nbd_refined0.172
r_symmetry_vdw_refined0.166
r_symmetry_hbond_refined0.142
r_metal_ion_refined0.074
r_chiral_restr0.053
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2340
Solvent Atoms2
Heterogen Atoms45

Software

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