2BF6

Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SLLPDB ENTRY 1SLL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1720 % PEG 3350, 0.2M POTASSIUM NITRATE, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.549

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.981α = 90
b = 69.413β = 90
c = 72.694γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2004-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
10.9757910.111.83.8290992
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)
10.971.03870.1953.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB ENTRY 1SLL0.97572647771308991.80.11330.11340.1331RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
113285.24037.5
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.11
s_zero_chiral_vol0.103
s_approx_iso_adps0.092
s_anti_bump_dis_restr0.081
s_from_restr_planes0.0348
s_similar_adp_cmpnt0.032
s_angle_d0.031
s_bond_d0.016
s_rigid_bond_adp_cmpnt0.006
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3524
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms35

Software

Software
Software NamePurpose
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing