6PO4 | pdb_00006po4

2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 14.5 mg/ml, 0.01M Tris pH 8.3; Screen: Classics II (B5), 1.26M Sodium phosphate, 0.14M Potassium phosphate; Cryo: 1:1, reservoir : 50% Sucrose.

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.536	α = 90
b = 214.743	β = 90
c = 146.904	γ = 90

Symmetry
Space Group	C 2 2 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 300 mm CCD	C(111)	2017-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	30	100	0.081	0.081	0.089	0.035	19.8	6.2		115902		-3	38.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		0.74	0.74	0.806	0.318	0.807	2.7	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	3o4v	2.1	29.87	108746	5621	99.92	0.1618	0.1603	0.17	0.1907	0.2	RANDOM	44.826

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]
-0.8			-2.38		3.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.623
r_dihedral_angle_4_deg	14.198
r_dihedral_angle_3_deg	10.014
r_dihedral_angle_1_deg	4.116
r_angle_refined_deg	1.363
r_angle_other_deg	0.325
r_gen_planes_refined	0.057
r_gen_planes_other	0.056
r_chiral_restr	0.055
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.623
r_dihedral_angle_4_deg	14.198
r_dihedral_angle_3_deg	10.014
r_dihedral_angle_1_deg	4.116
r_angle_refined_deg	1.363
r_angle_other_deg	0.325
r_gen_planes_refined	0.057
r_gen_planes_other	0.056
r_chiral_restr	0.055
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10256
Nucleic Acid Atoms
Solvent Atoms	784
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	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.