3RI6

A Novel Mechanism of Sulfur Transfer Catalyzed by O-Acetylhomoserine Sulfhydrylase in Methionine Biosynthetic Pathway of Wolinella succinogenes


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CB1PDB ENTRY 2CB1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1829525-30% (w/v) ethylene glycol and 5% (v/v) N-dodecyl-N, N-dimethylamine-N-oxide, pH 8, vapor diffusion, hanging drop, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.8α = 90
b = 62.5β = 120.5
c = 91.6γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702010-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F1CHESSF1

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
12.23096.80.1286.22.439656
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)
12.22.2498.60.4582.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2CB12.23038264201798.950.226150.224760.25085RANDOM23.575
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]
-2.06-1.231.07-0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.481
r_dihedral_angle_4_deg19.503
r_dihedral_angle_3_deg17.823
r_dihedral_angle_1_deg6.283
r_scangle_it4.755
r_scbond_it3.015
r_angle_refined_deg1.942
r_mcangle_it1.798
r_mcbond_it0.974
r_chiral_restr0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.481
r_dihedral_angle_4_deg19.503
r_dihedral_angle_3_deg17.823
r_dihedral_angle_1_deg6.283
r_scangle_it4.755
r_scbond_it3.015
r_angle_refined_deg1.942
r_mcangle_it1.798
r_mcbond_it0.974
r_chiral_restr0.147
r_bond_refined_d0.024
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5265
Nucleic Acid Atoms
Solvent Atoms183
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing