4E9A

Structure of Peptide Deformylase form Helicobacter Pylori in complex with inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2EW7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION7.5290HEPES, MPD, pH 7.5, EVAPORATION, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.3948.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.891α = 90
b = 52.057β = 90
c = 92.064γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.6634.48424141

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2EW71.66234.481.3524141122998.840.20880.20760.2302
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]
-0.480.38790.0921
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18
f_angle_d1.098
f_chiral_restr0.073
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1308
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms45

Software

Software
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling