1NC1

Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with 5'-methylthiotubercidin (MTH)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NC3PDB ENTRY 1NC3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.7293PEG 200, sodium acetate, sodium chloride, cobalt chloride, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.243.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.3α = 90
b = 69.3β = 90
c = 127.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C0.82650NSLSX8C

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
1247.5897.80.0624.830742512.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1398.94819

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NC3247.58530742152997.80.190.223RANDOM25
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]
2.23-1.46-0.77
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.6
c_angle_deg1.6
c_improper_angle_d0.94
c_bond_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3430
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms40

Software

Software
Software NamePurpose
CCDSYSdata collection
d*TREKdata reduction
CNSrefinement
CCDSYSdata reduction
d*TREKdata scaling
CNSphasing