2WKJ

Crystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex with pyruvate at 1.45A resolution in space group P212121


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NALPDB ENTRY 1NAL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.2100MM TRIS HCL, PH 8.2, 200MM AMMONIUM ACETATE, 18% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3447.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.329α = 90
b = 108.049β = 90
c = 148.309γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2007-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.4563.4296.20.0811.65.121322614.333
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)
11.451.5389.50.383.44.9

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 1NAL1.4587.332023611071895.860.167750.166650.18857RANDOM15.594
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]
-0.941.13-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.548
r_dihedral_angle_4_deg20.164
r_dihedral_angle_3_deg12.148
r_dihedral_angle_1_deg5.592
r_scangle_it2.899
r_scbond_it1.879
r_angle_refined_deg1.346
r_angle_other_deg1.268
r_mcangle_it0.984
r_mcbond_it0.592
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.548
r_dihedral_angle_4_deg20.164
r_dihedral_angle_3_deg12.148
r_dihedral_angle_1_deg5.592
r_scangle_it2.899
r_scbond_it1.879
r_angle_refined_deg1.346
r_angle_other_deg1.268
r_mcangle_it0.984
r_mcbond_it0.592
r_mcbond_other0.199
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d
r_gen_planes_other
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 Atoms9188
Nucleic Acid Atoms
Solvent Atoms1307
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing