2OMK | pdb_00002omk

Structure of the Bacteroides Thetaiotaomicron Thiamin Pyrophosphokinase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.7	295	0.05 M Potassium phosphate monobasic, 20 % w/v Polyethylene glycol 8000, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.309	α = 90
b = 66.084	β = 99.9
c = 57.552	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	Mirrors	2006-04-17	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARRESEARCH	Mirrors	2006-12-17	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 5ID-B	1.0000	APS	5ID-B
2	SYNCHROTRON	APS BEAMLINE 21-ID-D	0.9787	APS	21-ID-D

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	1.8	45	94.8	0.071	23.7	6.9	36873	36873		-3

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	1.8	1.86	67.1		0.3	5.5	4.5	2577

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	SAD	THROUGHOUT	1.8	30	34895	1829	95.02	0.1664	0.16454	0.1643	0.20025	0.2007	RANDOM	20.827

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]
0.81		0.46	-0.66		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.908
r_dihedral_angle_4_deg	15.551
r_dihedral_angle_3_deg	13.641
r_dihedral_angle_1_deg	5.964
r_scangle_it	3.096
r_scbond_it	2.027
r_mcangle_it	1.341
r_angle_refined_deg	1.094
r_mcbond_it	0.815
r_nbtor_refined	0.306
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.153
r_symmetry_hbond_refined	0.123
r_xyhbond_nbd_refined	0.112
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3344
Nucleic Acid Atoms
Solvent Atoms	490
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
SHELX	phasing
SHARP	phasing