4V3B

The structure of alpha2,3-sialyltransferase variant 1 from Pasteurella dagmatis in complex with the donor product CMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V2UPDB ENTRY 4V2U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.2 MG/ML PROTEIN CONCENTRATION 0.2 M AMMONIUM CHLORIDE, 20% W/V PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.555α = 90
b = 113.555β = 90
c = 65.74γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXEL2014-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.185099.30.099.53.2257841.2
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)
12.182.2697.70.891.23

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 4V2U2.185024101124999.980.189060.186440.23794RANDOM47.52
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]
1.010.51.01-3.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.18
r_dihedral_angle_3_deg16.889
r_dihedral_angle_4_deg13.492
r_dihedral_angle_1_deg6.909
r_mcangle_it5.355
r_scbond_it4.216
r_mcbond_it3.651
r_mcbond_other3.647
r_angle_refined_deg1.679
r_angle_other_deg0.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.18
r_dihedral_angle_3_deg16.889
r_dihedral_angle_4_deg13.492
r_dihedral_angle_1_deg6.909
r_mcangle_it5.355
r_scbond_it4.216
r_mcbond_it3.651
r_mcbond_other3.647
r_angle_refined_deg1.679
r_angle_other_deg0.831
r_chiral_restr0.098
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms3230
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing