5F9T

Crystal Structure of Streptococcus pneumoniae NanC, covalent complex with a fluorinated Neu5Ac derivative


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, 10% sugar free Irn Bru
Crystal Properties
Matthews coefficientSolvent content
2.8656.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.236α = 90
b = 74.843β = 96.31
c = 113.352γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2013-09-26MSINGLE 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
12.053097.70.1079.13.5102205
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)
12.052.0975.10.5762.83930

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 REPLACEMENTTHROUGHOUT2vw22.053096897509897.370.19950.19760.2348RANDOM33.251
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]
0.79-0.10.25-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.24
r_dihedral_angle_3_deg13.524
r_dihedral_angle_4_deg10.65
r_dihedral_angle_1_deg7.32
r_mcangle_it5.7
r_mcbond_it5.307
r_mcbond_other5.307
r_angle_refined_deg1.433
r_angle_other_deg1.094
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.24
r_dihedral_angle_3_deg13.524
r_dihedral_angle_4_deg10.65
r_dihedral_angle_1_deg7.32
r_mcangle_it5.7
r_mcbond_it5.307
r_mcbond_other5.307
r_angle_refined_deg1.433
r_angle_other_deg1.094
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10444
Nucleic Acid Atoms
Solvent Atoms553
Heterogen Atoms92

Software

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