2YIF

Crystal structure of a F. nucleatum FMN riboswitch - Free state


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 11% PEG-4000, 0.32 M MGCL2, AND 0.01 M TRIS-CL, PH 8.4
Crystal Properties
Matthews coefficientSolvent content
2.9164.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.472α = 90
b = 73.472β = 90
c = 135.168γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
13.34098.10.0922.95.966272113.49
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)
13.33.4290.10.482.84

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 3F2Q3.29829.844638335694.520.20870.20580.2572132.3
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]
-5.4284-5.42849.2468
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.898
f_angle_d0.517
f_chiral_restr0.053
f_plane_restr0.036
f_bond_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2374
Solvent Atoms26
Heterogen Atoms14

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
CNSphasing