4WKB

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 DROP295Protein (10 mg/mL); Reservoir (0.1M di-ammonium hydrogen citrate and 15% PEG 3350); Cryoprotection (20% (v/v) glycerol)
Crystal Properties
Matthews coefficientSolvent content
2.1141.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.192α = 90
b = 72.002β = 110.32
c = 61.648γ = 90
Symmetry
Space GroupP 1 21 1

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
11.3750930.04816.23.98503110.2
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)
11.371.3999.10.226.773.54510

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 REPLACEMENTTHROUGHOUT3DP91.373080872412692.950.16540.16450.183RANDOM13.758
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]
1.23-0.69-0.34-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.684
r_dihedral_angle_3_deg10.675
r_dihedral_angle_4_deg10.599
r_dihedral_angle_1_deg5.959
r_angle_refined_deg1.367
r_mcangle_it1.199
r_angle_other_deg0.755
r_mcbond_it0.724
r_mcbond_other0.724
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.684
r_dihedral_angle_3_deg10.675
r_dihedral_angle_4_deg10.599
r_dihedral_angle_1_deg5.959
r_angle_refined_deg1.367
r_mcangle_it1.199
r_angle_other_deg0.755
r_mcbond_it0.724
r_mcbond_other0.724
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3535
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms40

Software

Software
Software NamePurpose
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MOLREPphasing