4JE8

Crystal structure of a human-like mitochondrial peptide deformylase in complex with Met-Ala-Ser


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62935-15% PEG 5000 MME, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.55α = 90
b = 74.71β = 90
c = 109.76γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2009-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.45099.50.08411.684.21632622
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.392.5497.20.3863.034.2

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 DIFFRACTIONTHROUGHOUTPDB entry 1ZXZ2.446.68163268601000.177610.173810.25096RANDOM44.227
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]
-2.154.83-2.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.475
r_dihedral_angle_3_deg18.82
r_dihedral_angle_4_deg16.578
r_dihedral_angle_1_deg7.765
r_scangle_it4.896
r_scbond_it3.337
r_angle_refined_deg2.667
r_mcangle_it1.799
r_mcbond_it1.277
r_metal_ion_refined0.373
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.475
r_dihedral_angle_3_deg18.82
r_dihedral_angle_4_deg16.578
r_dihedral_angle_1_deg7.765
r_scangle_it4.896
r_scbond_it3.337
r_angle_refined_deg2.667
r_mcangle_it1.799
r_mcbond_it1.277
r_metal_ion_refined0.373
r_nbtor_refined0.312
r_symmetry_hbond_refined0.293
r_symmetry_vdw_refined0.231
r_nbd_refined0.229
r_xyhbond_nbd_refined0.183
r_chiral_restr0.143
r_bond_refined_d0.03
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3005
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing