4BWL

Structure of the Y137A mutant of E. coli N-acetylneuraminic acid lyase in complex with pyruvate, N-acetyl-D-mannosamine and N- acetylneuraminic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.2100MM TRIS-HCL PH 8.2, 200MM NACL, 18% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.4249.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.97α = 90
b = 143.22β = 109.51
c = 83.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-07-08MSINGLE 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
1249.598.70.099.63.682202221.4
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)
122.1195.70.412.83.5

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 2WNN249.4678080408498.070.182470.179640.2349RANDOM27.7
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]
50.39-7.26-24.13-26.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.238
r_dihedral_angle_4_deg18.903
r_dihedral_angle_3_deg15.342
r_dihedral_angle_1_deg6.439
r_scangle_it2.059
r_scbond_it1.383
r_angle_refined_deg1.342
r_angle_other_deg0.901
r_mcangle_it0.863
r_mcbond_it0.506
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.238
r_dihedral_angle_4_deg18.903
r_dihedral_angle_3_deg15.342
r_dihedral_angle_1_deg6.439
r_scangle_it2.059
r_scbond_it1.383
r_angle_refined_deg1.342
r_angle_other_deg0.901
r_mcangle_it0.863
r_mcbond_it0.506
r_mcbond_other0.117
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms9166
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing