2DRJ

Xray structure of alpha-2,3/8-sialyltransferase CstII F91Y mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RO7PDB entry 1RO7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52830.1M TEA pH 7.5, 20% PEG 400, 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties
Matthews coefficientSolvent content
2.4649.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.653α = 90
b = 116.653β = 90
c = 44.086γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2005-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.514

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
12.252594.30.06623.13.91345822
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)
2.252.3365.40.1853.1926

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1RO72.2523.8113478127936851000.1970.1970.1940.261RANDOM33.254
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]
-1.92-1.923.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.126
r_dihedral_angle_3_deg17.411
r_dihedral_angle_4_deg17.049
r_dihedral_angle_1_deg7.255
r_scangle_it4.183
r_scbond_it3.029
r_mcangle_it2.033
r_angle_refined_deg1.788
r_mcbond_it1.187
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.126
r_dihedral_angle_3_deg17.411
r_dihedral_angle_4_deg17.049
r_dihedral_angle_1_deg7.255
r_scangle_it4.183
r_scbond_it3.029
r_mcangle_it2.033
r_angle_refined_deg1.788
r_mcbond_it1.187
r_nbtor_refined0.322
r_nbd_refined0.223
r_symmetry_vdw_refined0.211
r_symmetry_hbond_refined0.199
r_xyhbond_nbd_refined0.197
r_chiral_restr0.125
r_bond_refined_d0.021
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1949
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms42

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing