2CKY | pdb_00002cky

Structure of the Arabidopsis thaliana thiamine pyrophosphate riboswitch with its regulatory ligand

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				10% 1,6-HEXANEDIOL 50MM SODIUM CACODYLATE PH7.0 10MM MGSO4

Crystal Properties
Matthews coefficient	Solvent content
2.57	51.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.85	α = 90
b = 98.67	β = 104.8
c = 54.55	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH			M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.9	15	96	0.235	0.175	7.6	3.7		8918		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	74		0.97	0.72	1.6	2.7

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.9	15	8918	1270	96	0.191	0.183	0.19	0.25	0.25	RANDOM	50.6

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]
1.62		0.88	-0.12		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	2.218
r_scangle_it	2.017
r_angle_other_deg	1.426
r_scbond_it	1.195
r_symmetry_vdw_other	0.392
r_nbtor_refined	0.252
r_nbd_other	0.247
r_xyhbond_nbd_refined	0.208
r_symmetry_vdw_refined	0.207
r_nbd_refined	0.178
r_symmetry_hbond_refined	0.17
r_nbtor_other	0.095
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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_scbond_other
r_scangle_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	3310
Solvent Atoms
Heterogen Atoms	74

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
SHELX	phasing
SHARP	phasing
REFMAC	refinement