2WNZ

Structure of the E192N mutant of E. coli N-acetylneuraminic acid lyase in complex with pyruvate in space group P21 crystal form I


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WNNPDB ENTRY 2WNN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18100MM TRIS-HCL PH 8.0, 200MM NACL, 18% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.448.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.921α = 90
b = 143.041β = 109.79
c = 83.918γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.8579.061000.07123.6107356222.176
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)
11.851.9599.90.432.53.5

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 2WNN1.8578.96101932538699.960.190250.188430.22525RANDOM23.034
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]
1.88-0.74-0.43-1.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.063
r_dihedral_angle_4_deg17.299
r_dihedral_angle_3_deg12.141
r_dihedral_angle_1_deg5.47
r_scangle_it2.261
r_scbond_it1.389
r_angle_refined_deg1.137
r_mcangle_it0.932
r_angle_other_deg0.845
r_mcbond_it0.507
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.063
r_dihedral_angle_4_deg17.299
r_dihedral_angle_3_deg12.141
r_dihedral_angle_1_deg5.47
r_scangle_it2.261
r_scbond_it1.389
r_angle_refined_deg1.137
r_mcangle_it0.932
r_angle_other_deg0.845
r_mcbond_it0.507
r_mcbond_other0.105
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms9215
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing