3N37

Ribonucleotide Reductase Dimanganese(II)-NrdF from Escherichia coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R2F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.1 M HEPES pH 7.5, 30% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.2261.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.142α = 90
b = 78.142β = 90
c = 266.754γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARMOSAIC 225 mm CCD2009-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

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
11.6567.67

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 REPLACEMENTTHROUGHOUT1R2F1.6567.6757359290297.010.1680.1670.185RANDOM19.543
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]
0.920.460.92-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.833
r_dihedral_angle_4_deg17.763
r_dihedral_angle_3_deg13.055
r_dihedral_angle_1_deg4.318
r_scangle_it3.013
r_scbond_it1.769
r_angle_refined_deg1.088
r_mcangle_it0.953
r_mcbond_it0.471
r_chiral_restr0.075
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.833
r_dihedral_angle_4_deg17.763
r_dihedral_angle_3_deg13.055
r_dihedral_angle_1_deg4.318
r_scangle_it3.013
r_scbond_it1.769
r_angle_refined_deg1.088
r_mcangle_it0.953
r_mcbond_it0.471
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2295
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction