4V2U

Apo-structure of alpha2,3-sialyltransferase from Pasteurella dagmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ILVPDB ENTRY 2ILV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.3 MG/ML OF PROTEIN INDEX SCREEN CONDITION D9 (0.1M TRIS PH 8.5, 25% W/V POLYETHYLENE GLYCOL 3350)
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.724α = 90
b = 56.59β = 111.95
c = 79.542γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPILATUS2014-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P11PETRA III, DESYP11

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
12.7145.198.80.1110.43.3126181.9
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)
12.712.8797.30.631.93.2

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 2ILV2.7145.111198763199.030.190180.18630.26099RANDOM46.174
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]
-0.890.64-1.781.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.47
r_dihedral_angle_3_deg18.993
r_dihedral_angle_4_deg18.976
r_dihedral_angle_1_deg6.32
r_mcangle_it5.004
r_scbond_it3.598
r_mcbond_other3.248
r_mcbond_it3.247
r_angle_refined_deg1.646
r_angle_other_deg0.818
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.47
r_dihedral_angle_3_deg18.993
r_dihedral_angle_4_deg18.976
r_dihedral_angle_1_deg6.32
r_mcangle_it5.004
r_scbond_it3.598
r_mcbond_other3.248
r_mcbond_it3.247
r_angle_refined_deg1.646
r_angle_other_deg0.818
r_chiral_restr0.082
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms3207
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing