4YW1

Crystal Structure of Streptococcus pneumoniae NanC, complex with Neu5Ac and Neu5Ac2en following soaking with 3'SL


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VW2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29816% PEG8000, 20% glycerol, 40mM monopotassium phosphate
Crystal Properties
Matthews coefficientSolvent content
2.8857.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.834α = 90
b = 74.945β = 96.35
c = 113.302γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2013-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
12.254094.50.1218.32.675606
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)
12.252.2997.80.4822.53900

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 REPLACEMENTTHROUGHOUT2vw22.254071657380394.150.21070.20870.2488RANDOM32.918
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]
-0.450.721.47-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.098
r_dihedral_angle_3_deg13.159
r_dihedral_angle_4_deg12.011
r_dihedral_angle_1_deg7.268
r_mcangle_it2.316
r_mcbond_it1.495
r_mcbond_other1.494
r_angle_refined_deg1.396
r_angle_other_deg1.056
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.098
r_dihedral_angle_3_deg13.159
r_dihedral_angle_4_deg12.011
r_dihedral_angle_1_deg7.268
r_mcangle_it2.316
r_mcbond_it1.495
r_mcbond_other1.494
r_angle_refined_deg1.396
r_angle_other_deg1.056
r_chiral_restr0.078
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10444
Nucleic Acid Atoms
Solvent Atoms857
Heterogen Atoms84

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction