3N39

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N373N37 and 1RLJ
experimental modelPDB 1RLJ3N37 and 1RLJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.620% PEG 3000, 0.1 M HEPES pH 7.6, 0.1 M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.2946.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.403α = 90
b = 90.721β = 90
c = 143.787γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARMOSAIC 225 mm CCD2009-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0781APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.533.84

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3N37 and 1RLJ2.533.8431363159590.540.2370.2350.273RANDOM58.999
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]
0.12-0.880.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.84
r_dihedral_angle_3_deg14.323
r_dihedral_angle_4_deg13.113
r_dihedral_angle_1_deg4.146
r_angle_refined_deg0.856
r_scangle_it0.632
r_mcangle_it0.376
r_scbond_it0.363
r_mcbond_it0.202
r_chiral_restr0.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.84
r_dihedral_angle_3_deg14.323
r_dihedral_angle_4_deg13.113
r_dihedral_angle_1_deg4.146
r_angle_refined_deg0.856
r_scangle_it0.632
r_mcangle_it0.376
r_scbond_it0.363
r_mcbond_it0.202
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6591
Nucleic Acid Atoms
Solvent Atoms20
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction