3N3B

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N39 

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.723α = 90
b = 91.348β = 90
c = 144.114γ = 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
12.3540.56

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 REPLACEMENTTHROUGHOUT3N392.3640.5639152195893.120.2360.2340.275RANDOM33.897
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]
0.25-0.24-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.763
r_dihedral_angle_3_deg13.952
r_dihedral_angle_4_deg11.211
r_dihedral_angle_1_deg4.022
r_angle_refined_deg0.819
r_scangle_it0.425
r_mcangle_it0.304
r_scbond_it0.24
r_mcbond_it0.165
r_chiral_restr0.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.763
r_dihedral_angle_3_deg13.952
r_dihedral_angle_4_deg11.211
r_dihedral_angle_1_deg4.022
r_angle_refined_deg0.819
r_scangle_it0.425
r_mcangle_it0.304
r_scbond_it0.24
r_mcbond_it0.165
r_chiral_restr0.053
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6650
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction