3H73

Crystal structure of Streptococcus pneumoniae D39 neuraminidase A precursor (NanA) in complex with DANA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7294100 mM Hepes, 30% Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.1542.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.34α = 90
b = 47.4β = 116.45
c = 137.32γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2008-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.981NSLSX4C

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
11.73093.20.0336.54139376211.6
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)
1.71.7686.20.07314.62.58694

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1.727.3493563703292.60.1780.1780.1780.209RANDOM14.6
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]
-1.611.440.850.76
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it2.6
c_scbond_it1.83
c_mcangle_it1.6
c_angle_deg1.3
c_mcbond_it1.05
c_improper_angle_d0.83
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25.7
c_scangle_it2.6
c_scbond_it1.83
c_mcangle_it1.6
c_angle_deg1.3
c_mcbond_it1.05
c_improper_angle_d0.83
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7518
Nucleic Acid Atoms
Solvent Atoms1539
Heterogen Atoms40

Software

Software
Software NamePurpose
ADSCdata collection
COMOphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling