5M63

Crystal structure of group B Streptococcus type III DP2 oligosaccharide bound to Fab NVS-1-19-5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62950.1 M Cadmium chloride hemi (pentahydrate), 30% (v/v) PEG 400, 0.1 M sodium acetate, pH 4.6 (Structure Screen 1 & 2 HT-96; Molecular Dimensions)
Crystal Properties
Matthews coefficientSolvent content
3.4264

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.341α = 90
b = 142.231β = 90
c = 144.732γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2016-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.7449.02990.080930.99812.124.53670267.72
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.742.838960.77610.6491.454.1

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 REPLACEMENTTHROUGHOUT4JO12.7449.0234868183499.180.237840.235520.28218RANDOM69.419
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]
-0.23-1.111.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.765
r_dihedral_angle_3_deg16.777
r_dihedral_angle_4_deg14.669
r_dihedral_angle_1_deg9.598
r_long_range_B_refined4.703
r_long_range_B_other4.686
r_mcangle_it2.746
r_mcangle_other2.746
r_scangle_other2.475
r_angle_refined_deg1.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.765
r_dihedral_angle_3_deg16.777
r_dihedral_angle_4_deg14.669
r_dihedral_angle_1_deg9.598
r_long_range_B_refined4.703
r_long_range_B_other4.686
r_mcangle_it2.746
r_mcangle_other2.746
r_scangle_other2.475
r_angle_refined_deg1.564
r_mcbond_it1.538
r_mcbond_other1.538
r_scbond_it1.464
r_scbond_other1.464
r_angle_other_deg0.928
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms6480
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms316

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing