3N3A

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1720% PEG 3000, 0.1 M HEPES pH 7, 0.2 M lithium sulfate, 3 mM sodium dithionite
Crystal Properties
Matthews coefficientSolvent content
2.2745.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.863α = 90
b = 90.678β = 90
c = 143.837γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARMOSAIC 225 mm CCD2010-03-08MSINGLE 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
11.9929.58

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 REPLACEMENTTHROUGHOUT3N391.9929.5867011340699.270.2040.2030.227RANDOM35.252
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_4_deg17.388
r_dihedral_angle_3_deg14.46
r_dihedral_angle_1_deg4.9
r_scangle_it2.381
r_scbond_it1.433
r_angle_refined_deg1.053
r_mcangle_it0.904
r_mcbond_it0.46
r_chiral_restr0.079
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.595
r_dihedral_angle_4_deg17.388
r_dihedral_angle_3_deg14.46
r_dihedral_angle_1_deg4.9
r_scangle_it2.381
r_scbond_it1.433
r_angle_refined_deg1.053
r_mcangle_it0.904
r_mcbond_it0.46
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6619
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction