3N3A

Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli in Complex with Reduced NrdI

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N39

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		20% PEG 3000, 0.1 M HEPES pH 7, 0.2 M lithium sulfate, 3 mM sodium dithionite

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.863	α = 90
b = 90.678	β = 90
c = 143.837	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	113	CCD	MARMOSAIC 225 mm CCD		2010-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0781	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.99	29.58

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3N39	1.99	29.58	67011	3406	99.27	0.204	0.203	0.227	RANDOM	35.252

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]
0.16			-0.01		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.595
r_dihedral_angle_4_deg	17.388
r_dihedral_angle_3_deg	14.46
r_dihedral_angle_1_deg	4.9
r_scangle_it	2.381
r_scbond_it	1.433
r_angle_refined_deg	1.053
r_mcangle_it	0.904
r_mcbond_it	0.46
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.595
r_dihedral_angle_4_deg	17.388
r_dihedral_angle_3_deg	14.46
r_dihedral_angle_1_deg	4.9
r_scangle_it	2.381
r_scbond_it	1.433
r_angle_refined_deg	1.053
r_mcangle_it	0.904
r_mcbond_it	0.46
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6619
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

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.