1ODZ

Expansion of the glycosynthase repertoire to produce defined manno-oligosaccharides


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J9YPDB ENTRY 1J9Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100MM TRIS 7.5, 26% PEG550, 9MM ZNSO4, 10MM MANNOTETRAOSE, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.855α = 90
b = 131.855β = 90
c = 54.268γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2001-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
11.41593.70.03629.54.01171242
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)
11.41.4564.40.3842.212.23

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 1J9Y1.430162650854593.70.1520.1510.177RANDOM13.6
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]
-0.52-0.521.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.164
r_scangle_it2.822
r_scbond_it1.932
r_mcangle_it1.401
r_angle_refined_deg1.4
r_angle_other_deg1.279
r_mcbond_it0.952
r_symmetry_vdw_other0.257
r_nbd_other0.254
r_nbd_refined0.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.164
r_scangle_it2.822
r_scbond_it1.932
r_mcangle_it1.401
r_angle_refined_deg1.4
r_angle_other_deg1.279
r_mcbond_it0.952
r_symmetry_vdw_other0.257
r_nbd_other0.254
r_nbd_refined0.218
r_symmetry_vdw_refined0.208
r_xyhbond_nbd_refined0.126
r_metal_ion_refined0.124
r_chiral_restr0.101
r_symmetry_hbond_refined0.099
r_nbtor_other0.088
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6065
Nucleic Acid Atoms
Solvent Atoms1033
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing