2VW2

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
19.510% PEG 8000, 0.15M NACL, 0.1M CHES PH 9.5
Crystal Properties
Matthews coefficientSolvent content
2.1943.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.642α = 90
b = 82.684β = 90
c = 116.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944MSINGLE 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
11.73092.10.088.9375667
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)
11.71.76630.362.23

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 1SLI1.767.42718463758920.1960.1940.229RANDOM18.51
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]
-0.5-0.841.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.022
r_dihedral_angle_3_deg12.31
r_dihedral_angle_4_deg11.128
r_dihedral_angle_1_deg6.364
r_scangle_it1.742
r_scbond_it1.106
r_angle_refined_deg1.099
r_mcangle_it0.796
r_mcbond_it0.463
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.022
r_dihedral_angle_3_deg12.31
r_dihedral_angle_4_deg11.128
r_dihedral_angle_1_deg6.364
r_scangle_it1.742
r_scbond_it1.106
r_angle_refined_deg1.099
r_mcangle_it0.796
r_mcbond_it0.463
r_nbtor_refined0.301
r_nbd_refined0.183
r_symmetry_vdw_refined0.136
r_xyhbond_nbd_refined0.122
r_symmetry_hbond_refined0.107
r_chiral_restr0.073
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms5189
Nucleic Acid Atoms
Solvent Atoms797
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing