2GDI | pdb_00002gdi

Crystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.9	293	28 % PEG4000, 100 mM Na-acetate, pH 4.8, and 200 mM NH4-acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.90

Crystal Properties
Matthews coefficient	Solvent content
2	38.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.819	α = 90
b = 29.558	β = 94.55
c = 95.17	γ = 90

Symmetry
Space Group	C 1 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 QUANTUM 315		2005-11-07	M	SINGLE WAVELENGTH
2	1	x-ray		CCD	ADSC QUANTUM 315		2005-11-07	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25		NSLS	X25
2	SYNCHROTRON	NSLS BEAMLINE X25	1.1407, 1.1411, 1.1201	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	2.05	20	99.8	0.062		4.3		27007

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	2.05	2.12	100		0.475	2.89	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	2.05	20	25309	25258	1337	99.8	0.21	0.208	0.21	0.241	0.24	RANDOM	34.95

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]
-0.76		-2.37	1.81		-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	1.196
r_angle_refined_deg	1.043
r_scbond_it	0.85
r_mcangle_it	0.435
r_nbtor_refined	0.284
r_mcbond_it	0.199
r_xyhbond_nbd_refined	0.191
r_symmetry_hbond_refined	0.177
r_nbd_refined	0.164
r_symmetry_vdw_refined	0.16
r_metal_ion_refined	0.141
r_chiral_restr	0.129
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d
r_angle_other_deg
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_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	3442
Solvent Atoms	312
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
CAD4	data reduction
HKL-2000	data scaling
SOLVE	phasing