4X24

Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with methylthio-DADMe-Immucillin-A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DP9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.3295Protein (10 mg/mL); Reservoir (0.2M ammonium chloride pH 6.3 and 20% PEG 3350); Cryoprotection (20% (v/v) glycerol)
Crystal Properties
Matthews coefficientSolvent content
2.244.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.898α = 90
b = 72.708β = 110
c = 61.621γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2014-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
11.55099.10.0828.93.66960213.2
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)
11.51.5396.80.6851.783.53351

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 REPLACEMENTTHROUGHOUT3DP91.53066097344899.090.16960.16870.1866RANDOM17.318
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]
1-0.24-0.12-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.259
r_dihedral_angle_4_deg13.133
r_dihedral_angle_3_deg11.333
r_dihedral_angle_1_deg5.866
r_angle_refined_deg1.455
r_mcangle_it1.403
r_angle_other_deg0.972
r_mcbond_it0.874
r_mcbond_other0.874
r_chiral_restr0.154
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.259
r_dihedral_angle_4_deg13.133
r_dihedral_angle_3_deg11.333
r_dihedral_angle_1_deg5.866
r_angle_refined_deg1.455
r_mcangle_it1.403
r_angle_other_deg0.972
r_mcbond_it0.874
r_mcbond_other0.874
r_chiral_restr0.154
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 Atoms3509
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms50

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction