Experiment: 2YIE

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F2Q	PDB ENTRY 3F2Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				RNA 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 coefficient	Solvent content
1.5	64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.679	α = 90
b = 73.679	β = 90
c = 139.251	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC CCD		2009-08-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.95	40	99.3	0.05	21.7	4.7		17834		2	80.36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.06	100		0.48	3.4	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 3F2Q	2.941	26.292	9559	507	98.03	0.2056	0.2041	0.2025	0.2314	96.2

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			-6.6226		13.2451

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	24.223
f_angle_d	0.612
f_chiral_restr	0.056
f_plane_restr	0.005
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	2394
Solvent Atoms	29
Heterogen Atoms	47

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
CNS	phasing