5WD7 | pdb_00005wd7

Structure of a bacterial polysialyltransferase in complex with fondaparinux


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29617% - 24% PEG3350 (v/v), 140 - 250 mM Mg2SO4 and 100 mM MES pH 7.2
Crystal Properties
Matthews coefficientSolvent content
2.9358

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.312α = 90
b = 78.312β = 90
c = 299.895γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-11.00635CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
13.144.931000.1370.1480.0540.99814.77.220333
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.311001.3921.4970.5450.5867.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.144.931933393899.90.18960.187250.20.238370.24RANDOM88.079
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]
-0.83-0.42-0.832.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.691
r_dihedral_angle_3_deg18.645
r_dihedral_angle_4_deg17.464
r_long_range_B_refined15.065
r_long_range_B_other15.065
r_scangle_other9.998
r_mcangle_it9.3
r_mcangle_other9.299
r_dihedral_angle_1_deg6.602
r_scbond_it6.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.691
r_dihedral_angle_3_deg18.645
r_dihedral_angle_4_deg17.464
r_long_range_B_refined15.065
r_long_range_B_other15.065
r_scangle_other9.998
r_mcangle_it9.3
r_mcangle_other9.299
r_dihedral_angle_1_deg6.602
r_scbond_it6.344
r_scbond_other6.343
r_mcbond_it6.002
r_mcbond_other6.002
r_angle_refined_deg1.603
r_angle_other_deg0.965
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6380
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms101

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing