2OSX

Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529420% (w/v) PEG 3350; 0.175 M NaCl; 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.244.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.801α = 90
b = 61.984β = 112.25
c = 102.846γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0000ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.131.73493.80.0540.0549.24.21717127.094
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.1689.90.4630.4631.54.223927

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.146.23171710869093.860.1220.1210.139RANDOM7.65
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]
0.080.03-0.190.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.712
r_dihedral_angle_4_deg12.93
r_dihedral_angle_3_deg11.374
r_sphericity_free6.678
r_dihedral_angle_1_deg6.178
r_sphericity_bonded3.68
r_scangle_it2.942
r_scbond_it2.206
r_mcangle_it1.742
r_angle_refined_deg1.468
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.712
r_dihedral_angle_4_deg12.93
r_dihedral_angle_3_deg11.374
r_sphericity_free6.678
r_dihedral_angle_1_deg6.178
r_sphericity_bonded3.68
r_scangle_it2.942
r_scbond_it2.206
r_mcangle_it1.742
r_angle_refined_deg1.468
r_mcbond_it1.159
r_rigid_bond_restr0.975
r_angle_other_deg0.955
r_mcbond_other0.596
r_symmetry_vdw_refined0.348
r_symmetry_vdw_other0.292
r_nbd_refined0.212
r_nbd_other0.207
r_nbtor_refined0.182
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.131
r_metal_ion_refined0.13
r_chiral_restr0.09
r_nbtor_other0.09
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3452
Nucleic Acid Atoms
Solvent Atoms598
Heterogen Atoms73

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing