3F2T

Crystal structure of the FMN riboswitch bound to FMN, iridium hexamine soak.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1 M MES-Na pH 6.5 10% PEG4000 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8156.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.493α = 90
b = 71.493β = 90
c = 138.718γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-12-02MMAD
21x-ray100CCDADSC QUANTUM 3152007-12-02MMAD
31x-ray100CCDADSC QUANTUM 3152007-12-02MMAD
1,2,31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C1.105275APS24-ID-C
2SYNCHROTRONAPS BEAMLINE 24-ID-C1.085914APS24-ID-C
3SYNCHROTRONAPS BEAMLINE 24-ID-C1.105462APS24-ID-C

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
1,2,3320990.09935.55.586158529
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)
1,2,333.1193.20.4593.15848

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 DIFFRACTIONMADTHROUGHOUT3208189807340098.580.210540.210540.20840.25212RANDOM111.245
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]
-3.05-1.53-3.054.58
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it1.389
r_angle_refined_deg0.989
r_scbond_it0.872
r_nbtor_refined0.281
r_nbd_refined0.183
r_xyhbond_nbd_refined0.162
r_symmetry_vdw_refined0.117
r_chiral_restr0.048
r_bond_refined_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2343
Solvent Atoms1
Heterogen Atoms116

Software

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