2YK7

Structure of Neisseria LOS-specific sialyltransferase (NST), in complex with CMP-3F-Neu5Ac.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YK4PDB ENTRY 2YK4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.4PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION METHODS USING DROPS OF PROTEIN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT: 180MM TRI-SODIUM CITRATE, 5 MM MNCL2, 20%(V/V) PEG 1500, PH 6.25 .
Crystal Properties
Matthews coefficientSolvent content
2.4449.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.762α = 90
b = 101.413β = 90
c = 166.57γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateX-RAY MIRRORS OSMIC VARIMAXHRMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.1883.3397.10.0123.97.6193772
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)
12.182.2284.90.052.645.4

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 2YK42.1883.331784495796.950.201030.198060.25786RANDOM29.876
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]
-0.881.1-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.084
r_dihedral_angle_4_deg18.324
r_dihedral_angle_3_deg16.665
r_dihedral_angle_1_deg5.977
r_scangle_it3.4
r_scbond_it2.425
r_angle_refined_deg1.765
r_mcangle_it1.563
r_mcbond_it0.908
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.084
r_dihedral_angle_4_deg18.324
r_dihedral_angle_3_deg16.665
r_dihedral_angle_1_deg5.977
r_scangle_it3.4
r_scbond_it2.425
r_angle_refined_deg1.765
r_mcangle_it1.563
r_mcbond_it0.908
r_chiral_restr0.112
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2612
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing