4WKC

Crystal structure of Escherichia coli 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with butylthio-DADMe-Immucillin-A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y6Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5295Protein (10 mg/mL); Reservoir (0.2M ammonium acetate, 0.1M BIS-TRIS pH5.5 and 25% PEG 3350); Cryoprotection (20% (v/v) glycerol)
Crystal Properties
Matthews coefficientSolvent content
2.2144.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.396α = 90
b = 91.386β = 90
c = 70.64γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.075NSLSX29A

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
11.645099.90.08311.211.52867713.5
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)
11.641.6798.30.5374.199.61394

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 REPLACEMENTTHROUGHOUT1Y6Q1.643027298134999.870.16060.15930.1857RANDOM18.061
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]
-0.740.170.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.752
r_dihedral_angle_4_deg19.456
r_dihedral_angle_3_deg10.989
r_dihedral_angle_1_deg5.881
r_mcangle_it1.536
r_angle_refined_deg1.378
r_mcbond_it0.956
r_mcbond_other0.95
r_angle_other_deg0.756
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.752
r_dihedral_angle_4_deg19.456
r_dihedral_angle_3_deg10.989
r_dihedral_angle_1_deg5.881
r_mcangle_it1.536
r_angle_refined_deg1.378
r_mcbond_it0.956
r_mcbond_other0.95
r_angle_other_deg0.756
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1708
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms36

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction