2VVZ

Structure of the catalytic domain of Streptococcus pneumoniae sialidase NanA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BF6PDB ENTRY 2BF6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.430% PEG 4000, 0.1M MES PH 6.4
Crystal Properties
Matthews coefficientSolvent content
2.3648

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.206α = 90
b = 95.626β = 90
c = 226.596γ = 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
12.530950.06272.936773
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)
12.52.54710.254.62.5

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 2BF62.53034868183096.40.2460.2430.298RANDOM37.32
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]
-0.290.72-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.184
r_dihedral_angle_4_deg14.829
r_dihedral_angle_3_deg14.443
r_dihedral_angle_1_deg7.367
r_angle_refined_deg1.145
r_scangle_it1.063
r_scbond_it0.642
r_mcangle_it0.633
r_mcbond_it0.358
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.184
r_dihedral_angle_4_deg14.829
r_dihedral_angle_3_deg14.443
r_dihedral_angle_1_deg7.367
r_angle_refined_deg1.145
r_scangle_it1.063
r_scbond_it0.642
r_mcangle_it0.633
r_mcbond_it0.358
r_nbtor_refined0.303
r_nbd_refined0.206
r_symmetry_vdw_refined0.187
r_xyhbond_nbd_refined0.145
r_symmetry_hbond_refined0.123
r_chiral_restr0.081
r_bond_refined_d0.007
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 Atoms7442
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing