4F1W

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with Adenine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O4V	pdb entry 3O4V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	1.0M (NH4)2HPO4, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.05	α = 90
b = 68.12	β = 90
c = 89.66	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	ADSC QUANTUM 315r	Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror	2011-08-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.36	54.24	100	0.112	0.112	12.9	11.5	87459	87459			12.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.36	1.43	99.9		2.6	11.2	12605

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3O4V	1.36	41.95	87381	83002	4379	99.94	0.11455	0.11455	0.11286	0.14597	RANDOM	15.932

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]
-0.63			-0.04		0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.373
r_dihedral_angle_2_deg	36.4
r_dihedral_angle_4_deg	19.272
r_dihedral_angle_3_deg	11.74
r_sphericity_bonded	10.401
r_dihedral_angle_1_deg	5.584
r_rigid_bond_restr	2.186
r_angle_refined_deg	1.435
r_angle_other_deg	0.812
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	38.373
r_dihedral_angle_2_deg	36.4
r_dihedral_angle_4_deg	19.272
r_dihedral_angle_3_deg	11.74
r_sphericity_bonded	10.401
r_dihedral_angle_1_deg	5.584
r_rigid_bond_restr	2.186
r_angle_refined_deg	1.435
r_angle_other_deg	0.812
r_chiral_restr	0.092
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3445
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	114

Software

Software
Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.