6VMY

Structure of the B. subtilis cobalamin riboswitch

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		287	Purified RNA was incubated at room temperature for 30 minutes in 25 mM Tris-HCl, pH 8.0, 50 mM potassium chloride, 10 mM magnesium chloride, 0.5 mM adenosylcobalamin prior to crystallization in 50 mM sodium cacodylate, 15% (v/v) PEG 400, 0.2 mM cobalt hexamine, 80 mM magnesium acetate, 1 mM spermine between pH 6.0 to pH 6.5 at 14C by vapor diffusion in a hanging drop format

Crystal Properties
Matthews coefficient	Solvent content
5.51	77.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.282	α = 90
b = 118.282	β = 90
c = 261.547	γ = 120

Symmetry
Space Group	P 65 2 2

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	RAYONIX MX-225	Mirrors	2013-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	3.253	39.213	92.8	0.16	0.162	0.025	0.996	18.2	47		15338

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.28	3.46	43.8		4.129	4.168	0.561	0.598		54

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	FREE R-VALUE	3.25	39.21	15338	785	86.3	0.263	0.279	129.1

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]
0.693	0.347		0.693		-2.248

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.013
r_scangle_other	3.118
r_scangle_it	3.117
r_angle_other_deg	2.165
r_scbond_it	1.847
r_scbond_other	1.847
r_dihedral_angle_3_deg	1.736
r_angle_refined_deg	0.807
r_nbtor_refined	0.253
r_nbd_other	0.22
r_xyhbond_nbd_refined	0.208
r_nbd_refined	0.148
r_chiral_restr	0.074
r_gen_planes_refined	0.033
r_gen_planes_other	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	3174
Solvent Atoms	48
Heterogen Atoms	179

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHARP	phasing
Coot	model building