2VW0

Crystal structure of the NanB sialidase from Streptococcus pneumoniae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SLIPDB ENTRY 1SLI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
187% PEG 8000, 0.1M IMIDAZOLE PH 8
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.36α = 90
b = 83.417β = 90
c = 120.149γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.330980.1113.96.134651
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)
12.32.38950.464.86

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 1SLI2.34032865173398.10.1750.1720.232RANDOM26.67
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]
-1.91-1.513.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.406
r_dihedral_angle_3_deg13.877
r_dihedral_angle_4_deg13.501
r_dihedral_angle_1_deg6.671
r_scangle_it2.431
r_scbond_it1.566
r_angle_refined_deg1.298
r_mcangle_it1.088
r_mcbond_it0.642
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.406
r_dihedral_angle_3_deg13.877
r_dihedral_angle_4_deg13.501
r_dihedral_angle_1_deg6.671
r_scangle_it2.431
r_scbond_it1.566
r_angle_refined_deg1.298
r_mcangle_it1.088
r_mcbond_it0.642
r_nbtor_refined0.297
r_symmetry_vdw_refined0.272
r_symmetry_hbond_refined0.248
r_nbd_refined0.179
r_xyhbond_nbd_refined0.172
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms5181
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing