4V39

Apo-structure of alpha2,3-sialyltransferase variant 2 from Pasteurella dagmatis


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.7 MG/ML PROTEIN CONCENTRATION 0.1M CITRATE, 20%W/V PEG 6000, PH 5.0
Crystal Properties
Matthews coefficientSolvent content
2.653

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.19α = 90
b = 56.85β = 111.35
c = 79.68γ = 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
12.3452.399.20.1310.94.8226482.1
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)
12.342.5299.40.812.14.9

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 4V2U2.674.211364971399.340.194630.191130.2632RANDOM36.837
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]
0.22-0.97-0.280.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.492
r_dihedral_angle_3_deg16.563
r_dihedral_angle_4_deg14.768
r_dihedral_angle_1_deg6.559
r_mcangle_it3.337
r_scbond_it2.178
r_mcbond_it1.974
r_mcbond_other1.974
r_angle_refined_deg1.31
r_angle_other_deg0.734
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.492
r_dihedral_angle_3_deg16.563
r_dihedral_angle_4_deg14.768
r_dihedral_angle_1_deg6.559
r_mcangle_it3.337
r_scbond_it2.178
r_mcbond_it1.974
r_mcbond_other1.974
r_angle_refined_deg1.31
r_angle_other_deg0.734
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms3227
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing