3N39 | pdb_00003n39

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3N37	3N37 and 1RLJ
experimental model	PDB	1RLJ	3N37 and 1RLJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.6		20% PEG 3000, 0.1 M HEPES pH 7.6, 0.1 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.403	α = 90
b = 90.721	β = 90
c = 143.787	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		2009-12-21	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	2.5	33.84

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	3N37 and 1RLJ	2.5	33.84	31363	1595	90.54	0.237	0.235	0.23	0.273	0.27	RANDOM	58.999

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]
0.12			-0.88		0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.84
r_dihedral_angle_3_deg	14.323
r_dihedral_angle_4_deg	13.113
r_dihedral_angle_1_deg	4.146
r_angle_refined_deg	0.856
r_scangle_it	0.632
r_mcangle_it	0.376
r_scbond_it	0.363
r_mcbond_it	0.202
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.84
r_dihedral_angle_3_deg	14.323
r_dihedral_angle_4_deg	13.113
r_dihedral_angle_1_deg	4.146
r_angle_refined_deg	0.856
r_scangle_it	0.632
r_mcangle_it	0.376
r_scbond_it	0.363
r_mcbond_it	0.202
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6591
Nucleic Acid Atoms
Solvent Atoms	20
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.