3O0N

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and Adenosylcobalamin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XJEPDB entry 1XJE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529310% PEG8000, 0.1M sodium acetate, 0.1 M sodium chloride, 10mM DTT (dithiotreithol), 5% glycerol, crystallization geometry: 4 microL protein 11miligram/milliL + 2uL reservoir solution over 300 microL in 24-well plate. Crystals in 3-4 days, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.652.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.01α = 90
b = 123.82β = 103.1
c = 106.44γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.931ESRFID14-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.9520990.0920.10194.4510810030.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9520.0880.8050.01593.87919

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONRIGID BODY REFINEMENTPDB entry 1XJE1.9519.97108084540799.150.20490.20250.2493
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]
2.72396.45073.3735-6.0974
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.178
f_angle_d1.081
f_chiral_restr0.071
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9782
Nucleic Acid Atoms
Solvent Atoms513
Heterogen Atoms171

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing