4JOS | pdb_00004jos

Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Francisella philomiragia ATCC 25017 (Target NYSGRC-029335)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT); Reservoir (MCSG1 #13; G10: 0.6 M Sodium Chloride, 0.1 M MES:NaOH pH 6.5, 20% (w/v) PEG 4000 )); Cryoprotection (30% Ethylene glycol), temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.747	α = 90
b = 74.937	β = 90
c = 114.542	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	RAYONIX MX225HE	MIRRORS	2013-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	1.45	50	99.7	0.119	21.06	14.8		85555			12.3

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)
1	1.45	1.48	99.2		0.847	2.88	14.5	4211

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	1.45	29.06	85484	2164	99.68	0.152	0.1514	0.1514	0.1747	0.1747	RANDOM	16.2734

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]
1.04			-0.04		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.773
r_dihedral_angle_4_deg	15.19
r_dihedral_angle_3_deg	12.913
r_dihedral_angle_1_deg	5.812
r_angle_refined_deg	1.504
r_angle_other_deg	0.777
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.773
r_dihedral_angle_4_deg	15.19
r_dihedral_angle_3_deg	12.913
r_dihedral_angle_1_deg	5.812
r_angle_refined_deg	1.504
r_angle_other_deg	0.777
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3525
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

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.