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Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with actinonin (crystallized in PEG-550-MME)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PN2 PDB ENTRY 3PN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG-550-MME, Zinc sulfate 25mM, 70mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.57 α = 90 b = 56.57 β = 90 c = 146.11 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2009-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 50 99.7 0.059 18.95 4.4 18505 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.02 99.8 0.335 4.14 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT PDB ENTRY 3PN2 1.9 40 18505 974 100 0.18322 0.18184 0.1926 0.20988 0.2208 RANDOM 18.274
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] 0.57 0.57 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.048 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_1_deg 5.582 r_scangle_it 3.224 r_scbond_it 2.13 r_angle_refined_deg 1.387 r_mcangle_it 1.157 r_mcbond_it 0.785 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.048 r_dihedral_angle_4_deg 18.649 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_1_deg 5.582 r_scangle_it 3.224 r_scbond_it 2.13 r_angle_refined_deg 1.387 r_mcangle_it 1.157 r_mcbond_it 0.785 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.227 r_xyhbond_nbd_refined 0.224 r_symmetry_metal_ion_refined 0.221 r_nbd_refined 0.217 r_metal_ion_refined 0.196 r_symmetry_vdw_refined 0.186 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 1401 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 32
Software Software Software Name Purpose ADSC data collection REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing