3NO6 | pdb_00003no6

Crystal structure of a putative thiaminase II (SE1693) from Staphylococcus epidermidis ATCC 12228 at 1.65 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	24.8000% 2-methyl-2,4-pentanediol, 0.2000M ammonium acetate, 0.1M sodium citrate - citric acid pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.155	α = 90
b = 92.713	β = 90
c = 165.037	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2010-03-12	M	MAD
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2010-02-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.00000	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97947	SSRL	BL11-1

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
1,2	1.65	29.867	99.7	0.069		3.7		129347			21.666

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	1.65	29.867	129279	6507	99.55	0.167	0.166	0.18	0.19	0.2	RANDOM	27.898

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]
0.27			0.17		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.351
r_dihedral_angle_4_deg	13.94
r_dihedral_angle_3_deg	11.565
r_scangle_it	3.883
r_dihedral_angle_1_deg	3.409
r_scbond_it	2.423
r_angle_refined_deg	1.605
r_mcangle_it	1.478
r_angle_other_deg	1.288
r_mcbond_it	0.814

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.351
r_dihedral_angle_4_deg	13.94
r_dihedral_angle_3_deg	11.565
r_scangle_it	3.883
r_dihedral_angle_1_deg	3.409
r_scbond_it	2.423
r_angle_refined_deg	1.605
r_mcangle_it	1.478
r_angle_other_deg	1.288
r_mcbond_it	0.814
r_mcbond_other	0.237
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7431
Nucleic Acid Atoms
Solvent Atoms	780
Heterogen Atoms	129

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.