2YIE

Crystal structure of a F. nucleatum FMN riboswitch bound to FMN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F2QPDB ENTRY 3F2Q

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1RNA WAS CRYSTALLIZED FROM 15% PEG-MONOMETHYL 550 ETHER, 0.1 M MGCL2, 0.05 M NA-HEPES PH 7.0, 1 MM FMN
Crystal Properties
Matthews coefficientSolvent content
1.564

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.679α = 90
b = 73.679β = 90
c = 139.251γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X25NSLSX25

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
12.954099.30.0521.74.717834280.36
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)
12.953.061000.483.43.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 3F2Q2.94126.292955950798.030.20560.20410.231496.2
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]
-6.6226-6.622613.2451
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d24.223
f_angle_d0.612
f_chiral_restr0.056
f_plane_restr0.005
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2394
Solvent Atoms29
Heterogen Atoms47

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
CNSphasing