5BO6

Structure of human sialyltransferase ST8SiaIII in complex with CDP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.82930.2 M (NH4)3PO4, 50 mM PIPES, 18-22% PEG2000
Crystal Properties
Matthews coefficientSolvent content
2.7555.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.928α = 90
b = 96.867β = 90
c = 124.981γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2014-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-10.97947CLSI08B1-1

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
12.0758.2698.90.0550.0240.99922.3653860
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)
12.072.1395.50.6490.3180.8332.74.93984

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 REPLACEMENTTHROUGHOUT5BO82.0758.2651139267098.410.16940.16770.2017RANDOM39.925
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]
2.12-0.08-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.169
r_dihedral_angle_4_deg19.651
r_dihedral_angle_3_deg15.158
r_dihedral_angle_1_deg6.42
r_mcangle_it2.847
r_angle_refined_deg2.023
r_mcbond_it1.96
r_mcbond_other1.945
r_angle_other_deg1.58
r_chiral_restr0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.169
r_dihedral_angle_4_deg19.651
r_dihedral_angle_3_deg15.158
r_dihedral_angle_1_deg6.42
r_mcangle_it2.847
r_angle_refined_deg2.023
r_mcbond_it1.96
r_mcbond_other1.945
r_angle_other_deg1.58
r_chiral_restr0.132
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_bond_other_d0.009
r_gen_planes_other0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4683
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms267

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata scaling