3O0Q

Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP, GDP and Adenosine


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
2.6253.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.12α = 90
b = 124.38β = 103.43
c = 106.82γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-05-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-50.969MAX III911-5

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.825990.0753.13139747138378
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.999.90.4742.243.13

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONRigid Body refinementPDB entry 1XJE1.823.119139747138344694299.080.1780.17630.2099
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]
6.10316.26850.9937-7.0968
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.268
f_angle_d1.086
f_chiral_restr0.076
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9916
Nucleic Acid Atoms
Solvent Atoms905
Heterogen Atoms155

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing