2P2V

Crystal structure analysis of monofunctional alpha-2,3-sialyltransferase Cst-I from Campylobacter jejuni


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RO7PDB 1RO7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.520mM Tris-HCl pH 7.5, and 200mM NaCl
Crystal Properties
Matthews coefficientSolvent content
2.8156.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.388α = 90
b = 112.388β = 90
c = 58.757γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210KOHZU: Double Crystal Si(111)2004-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.1ALS8.2.1

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
11.75099.80.06421.410.59405932
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)
1.71.76990.5242.63965

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB 1RO71.8539.75405933136215651000.2040.2040.2020.242RANDOM37.449
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]
-0.02-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.152
r_dihedral_angle_4_deg16.891
r_dihedral_angle_3_deg13.642
r_dihedral_angle_1_deg6.071
r_scangle_it3.867
r_scbond_it2.661
r_angle_refined_deg1.994
r_mcangle_it1.924
r_mcbond_it1.181
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.152
r_dihedral_angle_4_deg16.891
r_dihedral_angle_3_deg13.642
r_dihedral_angle_1_deg6.071
r_scangle_it3.867
r_scbond_it2.661
r_angle_refined_deg1.994
r_mcangle_it1.924
r_mcbond_it1.181
r_nbtor_refined0.315
r_symmetry_vdw_refined0.222
r_nbd_refined0.212
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.137
r_chiral_restr0.125
r_bond_refined_d0.019
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2285
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms91

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction