3N38

Ribonucleotide Reductase NrdF from Escherichia coli Soaked with Ferrous Ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N37 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.625% PEG 4000, 0.1 M HEPES pH 7.6, 0.1 M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.3262.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.137α = 90
b = 79.137β = 90
c = 267.981γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDMARMOSAIC 225 mm CCD2010-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.03324APS21-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
11.968.53

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 REPLACEMENTTHROUGHOUT3N371.968.5338952195697.30.1970.1960.22RANDOM34.621
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]
0.980.490.98-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.899
r_dihedral_angle_4_deg20.556
r_dihedral_angle_3_deg12.157
r_dihedral_angle_1_deg4.618
r_scangle_it2.998
r_scbond_it1.723
r_angle_refined_deg1.004
r_mcangle_it0.911
r_mcbond_it0.442
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.899
r_dihedral_angle_4_deg20.556
r_dihedral_angle_3_deg12.157
r_dihedral_angle_1_deg4.618
r_scangle_it2.998
r_scbond_it1.723
r_angle_refined_deg1.004
r_mcangle_it0.911
r_mcbond_it0.442
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2277
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction