3O3J

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with inhibitor 6b


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M6O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG550MME, ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7254.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.5α = 90
b = 57.5β = 90
c = 144.84γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002008-10-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.98SOLEILPROXIMA 1

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
133598.10.04613.51.99287911322
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)
133.1898.10.24131.91460

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 REPLACEMENTTHROUGHOUT3M6O328.7591135261000.209020.200430.28506RANDOM73.294
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]
2.922.92-5.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.526
r_dihedral_angle_4_deg28.056
r_dihedral_angle_3_deg27.313
r_dihedral_angle_1_deg9.665
r_scangle_it6.355
r_scbond_it4.172
r_angle_refined_deg3.918
r_mcangle_it2.234
r_mcbond_it1.343
r_symmetry_vdw_refined0.384
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.526
r_dihedral_angle_4_deg28.056
r_dihedral_angle_3_deg27.313
r_dihedral_angle_1_deg9.665
r_scangle_it6.355
r_scbond_it4.172
r_angle_refined_deg3.918
r_mcangle_it2.234
r_mcbond_it1.343
r_symmetry_vdw_refined0.384
r_nbtor_refined0.377
r_nbd_refined0.344
r_symmetry_hbond_refined0.277
r_metal_ion_refined0.243
r_xyhbond_nbd_refined0.234
r_chiral_restr0.207
r_bond_refined_d0.05
r_gen_planes_refined0.011
r_symmetry_metal_ion_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1377
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms21

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling