3M6P

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with actinonin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M6OPDB entry 3M6O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29314% PEG-3350, 0.2M zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6553.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.56α = 90
b = 56.47β = 90
c = 145.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9797ESRFBM30A

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
125098.90.10113.577.7324123204922
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)
122.1293.20.388574790

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 DIFFRACTIONrigid bodyTHROUGHOUTPDB entry 3M6O25030382162398.790.217360.214840.26454RANDOM26.086
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]
1.340.51-1.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.388
r_dihedral_angle_4_deg23.556
r_dihedral_angle_3_deg16.96
r_dihedral_angle_1_deg6.831
r_scangle_it4.107
r_scbond_it3.052
r_angle_refined_deg1.964
r_mcangle_it1.69
r_mcbond_it1.214
r_symmetry_hbond_refined0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.388
r_dihedral_angle_4_deg23.556
r_dihedral_angle_3_deg16.96
r_dihedral_angle_1_deg6.831
r_scangle_it4.107
r_scbond_it3.052
r_angle_refined_deg1.964
r_mcangle_it1.69
r_mcbond_it1.214
r_symmetry_hbond_refined0.335
r_symmetry_vdw_refined0.33
r_nbtor_refined0.314
r_nbd_refined0.237
r_xyhbond_nbd_refined0.22
r_chiral_restr0.113
r_metal_ion_refined0.105
r_bond_refined_d0.022
r_symmetry_metal_ion_refined0.02
r_gen_planes_refined0.008
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_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2798
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms63

Software

Software
Software NamePurpose
ADSCdata collection
CNSrefinement
REFMACrefinement
XDSdata reduction
XDSdata scaling
CNSphasing