3K0J | pdb_00003k0j

Crystal structure of the E. coli ThiM riboswitch in complex with thiamine pyrophosphate and the U1A crystallization module

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	298	20% (v/v) PEG 550 MME, 20% MPD, and 80 mM sodium citrate (pH 5.6), VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.25	α = 90
b = 71.6	β = 94.62
c = 128.35	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	ADSC QUANTUM 315	vertically collimating premirror, LN2 cooled double-crystal silicon (111) monochromator, toroidal focusing M2 mirror		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2		ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.1	30		0.169	9.3	4.4	17454	17359

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.1	3.2			0.556	2.6	4.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	3.1	29.5	16145	1595	93.1	0.197	0.197	0.2	0.279	0.28	RANDOM	42.6

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]
-4.38		1.04	9.21		-4.82

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.2
c_scangle_it	6.88
c_mcangle_it	5.36
c_scbond_it	4.76
c_mcbond_it	3.33
c_improper_angle_d	2.53
c_angle_deg	1.9
c_bond_d	0.978
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2775
Nucleic Acid Atoms	3642
Solvent Atoms
Heterogen Atoms	60

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction