2WNN

Structure of wild type E. coli N-acetylneuraminic acid lyase in complex with pyruvate in space group P21


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WKJPDB ENTRY 2WKJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.2100 MM TRIS-HCL PH 8.2, 200 MM NACL, 18 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.693α = 90
b = 142.456β = 109.16
c = 83.626γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.6579.0691.20.0613.53.4131694219.85
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)
11.651.7460.80.323.22.9

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 2WKJ1.6579.07125055659690.560.211830.209860.2492RANDOM18.189
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]
20.224.67-3.37-16.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.871
r_dihedral_angle_4_deg20.705
r_dihedral_angle_3_deg13.992
r_dihedral_angle_1_deg6.112
r_scangle_it2.434
r_scbond_it1.736
r_angle_refined_deg1.404
r_mcangle_it1.097
r_angle_other_deg0.93
r_mcbond_it0.683
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.871
r_dihedral_angle_4_deg20.705
r_dihedral_angle_3_deg13.992
r_dihedral_angle_1_deg6.112
r_scangle_it2.434
r_scbond_it1.736
r_angle_refined_deg1.404
r_mcangle_it1.097
r_angle_other_deg0.93
r_mcbond_it0.683
r_mcbond_other0.186
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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 Atoms9120
Nucleic Acid Atoms
Solvent Atoms758
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing