2ZBT

Crystal structure of pyridoxine biosynthesis protein from Thermus thermophilus HB8

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	293	0.1M Magnesium acetate, 0.1M Sodium cacodylate pH6.7, 22.5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.97	α = 90
b = 180.97	β = 90
c = 100.75	γ = 120

Symmetry
Space Group	H 3

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	RIGAKU JUPITER 210		2005-12-09	M	MAD
2	1	x-ray	100	CCD	RIGAKU JUPITER 210		2006-05-22	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	0.97904, 0.9000, 0.97942	SPring-8	BL26B2
2	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.0000	SPring-8	BL26B2

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	1.65	50	100	0.04	52.73	7.4		148066			18.8

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	1.65	1.71	100		0.221	6.2	6.7

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.65	47.96	148028	14786	99.8	0.194	0.194	0.21	RANDOM	21.4

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]
0.53	1.11		0.53		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.2
c_scangle_it	2.66
c_scbond_it	1.83
c_mcangle_it	1.71
c_angle_deg	1.4
c_mcbond_it	1.08
c_improper_angle_d	0.8
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8318
Nucleic Acid Atoms
Solvent Atoms	622
Heterogen Atoms	32

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.