4V38 | pdb_00004v38

Apo-structure of alpha2,3-sialyltransferase variant 1 from Pasteurella dagmatis


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 OF PROTEIN 0.1M SUCCINIC ACID, 15% W/V PEG 3350, PH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.22α = 90
b = 57.09β = 111.36
c = 80.15γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.8375980.0611.94.7409971.4
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)
11.831.987.30.871.43.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4V2U1.9674.6532268163599.380.1930.190410.20.244130.25RANDOM43.776
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]
-0.02-0.26-1.181.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.101
r_dihedral_angle_3_deg15.5
r_dihedral_angle_4_deg14.74
r_long_range_B_refined7.955
r_long_range_B_other7.95
r_dihedral_angle_1_deg6.631
r_scangle_other6.228
r_mcangle_it4.461
r_mcangle_other4.46
r_scbond_it4.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.101
r_dihedral_angle_3_deg15.5
r_dihedral_angle_4_deg14.74
r_long_range_B_refined7.955
r_long_range_B_other7.95
r_dihedral_angle_1_deg6.631
r_scangle_other6.228
r_mcangle_it4.461
r_mcangle_other4.46
r_scbond_it4.004
r_scbond_other4.003
r_mcbond_it3.345
r_mcbond_other3.338
r_angle_refined_deg1.535
r_angle_other_deg0.802
r_chiral_restr0.092
r_bond_refined_d0.013
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_scangle_it
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 Atoms127
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing