2XFW

Structure of the E192N mutant of E. coli N-acetylneuraminic acid lyase in complex with pyruvate in crystal form III


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.2100MM TRIS-HCL PH 8.2, 200MM NACL, 18% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5151.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.11α = 90
b = 116.53β = 117.95
c = 83.74γ = 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
11.6537.031000.0910.93.7158593214.5
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)
11.651.7499.90.442.83.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WNN1.6573.98150598796099.10.157720.156460.160.181640.19RANDOM10.922
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]
1.850.55.96-7.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.004
r_dihedral_angle_4_deg17.883
r_dihedral_angle_3_deg12.185
r_dihedral_angle_1_deg5.62
r_scangle_it3.022
r_scbond_it1.897
r_angle_refined_deg1.272
r_mcangle_it1.129
r_angle_other_deg0.898
r_mcbond_it0.64
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9264
Nucleic Acid Atoms
Solvent Atoms977
Heterogen Atoms67

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing