5BO9

Structure of human sialyltransferase ST8SiaIII in complex with CMP-3FNeu5Ac and Sia-6S-LacNAc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5BO8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529318-21% PEG3350, 30 mM sodium tartrate, 100 mM sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.5150.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.35α = 90
b = 94.874β = 90
c = 126.459γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.375.891000.0870.0440.99812.34.834645
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.381000.6860.3470.6742.24.93345

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 REPLACEMENTTHROUGHOUT5BO82.375.8932842174399.920.18710.18470.2304RANDOM43.944
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]
1.1-1.280.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.967
r_dihedral_angle_4_deg18.944
r_dihedral_angle_3_deg15.197
r_dihedral_angle_1_deg6.006
r_mcangle_it3.034
r_mcbond_it1.984
r_mcbond_other1.982
r_angle_refined_deg1.872
r_angle_other_deg1.107
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.967
r_dihedral_angle_4_deg18.944
r_dihedral_angle_3_deg15.197
r_dihedral_angle_1_deg6.006
r_mcangle_it3.034
r_mcbond_it1.984
r_mcbond_other1.982
r_angle_refined_deg1.872
r_angle_other_deg1.107
r_chiral_restr0.096
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4640
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms342

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing