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Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with inhibitor 6b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3M6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG550MME, ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.5 α = 90 b = 57.5 β = 90 c = 144.84 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 2008-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98 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 3 35 98.1 0.046 13.5 1.9 9287 9113 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 3 3.18 98.1 0.241 3 1.9 1460
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 3M6O 3 28.75 9113 526 100 0.20902 0.20043 0.2277 0.28506 0.2876 RANDOM 73.294
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] 2.92 2.92 -5.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.526 r_dihedral_angle_4_deg 28.056 r_dihedral_angle_3_deg 27.313 r_dihedral_angle_1_deg 9.665 r_scangle_it 6.355 r_scbond_it 4.172 r_angle_refined_deg 3.918 r_mcangle_it 2.234 r_mcbond_it 1.343 r_symmetry_vdw_refined 0.384
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.526 r_dihedral_angle_4_deg 28.056 r_dihedral_angle_3_deg 27.313 r_dihedral_angle_1_deg 9.665 r_scangle_it 6.355 r_scbond_it 4.172 r_angle_refined_deg 3.918 r_mcangle_it 2.234 r_mcbond_it 1.343 r_symmetry_vdw_refined 0.384 r_nbtor_refined 0.377 r_nbd_refined 0.344 r_symmetry_hbond_refined 0.277 r_metal_ion_refined 0.243 r_xyhbond_nbd_refined 0.234 r_chiral_restr 0.207 r_bond_refined_d 0.05 r_gen_planes_refined 0.011 r_symmetry_metal_ion_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1377 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 21
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling