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Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) (crystallized in PEG-550-MME)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M6O PDB entry 3M6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG-550-MME, Zinc sulfate 75mM, 70mM MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.32 α = 90 b = 56.32 β = 90 c = 148.44 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 2008-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980 SOLEIL PROXIMA 1
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 2 30 98.8 0.05 12.6 2.5 15978 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 2 2.12 98.9 0.409 2.65 2.5 4882
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 MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3M6O 2 30 15978 841 100 0.20525 0.20256 0.2147 0.25751 0.2699 RANDOM 45.124
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] 1.77 1.77 -3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 17.519 r_dihedral_angle_1_deg 6.119 r_scangle_it 4.16 r_scbond_it 2.862 r_angle_refined_deg 1.879 r_mcangle_it 1.521 r_mcbond_it 1.069 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.86 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 17.519 r_dihedral_angle_1_deg 6.119 r_scangle_it 4.16 r_scbond_it 2.862 r_angle_refined_deg 1.879 r_mcangle_it 1.521 r_mcbond_it 1.069 r_nbtor_refined 0.313 r_symmetry_metal_ion_refined 0.307 r_xyhbond_nbd_refined 0.25 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.225 r_metal_ion_refined 0.161 r_chiral_restr 0.131 r_symmetry_hbond_refined 0.126 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 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 1402 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 6
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling