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Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) in complex with inhibitor 21
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 17% PEG-3350, Zinc acetate 200mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.6 α = 90 b = 55.61 β = 90 c = 149.53 γ = 90
Symmetry Space Group P 21 21 21
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 315 2007-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.970 ESRF ID29
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 1.3 50 98.5 0.066 19.33 8 114769 113073 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 1.3 1.38 96.9 0.398 5.13 8.1 18312
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 rigid body THROUGHOUT PDB entry 3M6O 1.3 44.62 107411 5659 98.57 0.15996 0.15945 0.1601 0.16948 0.1635 RANDOM 13.993
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] -0.08 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.871 r_dihedral_angle_4_deg 15.25 r_dihedral_angle_3_deg 10.656 r_dihedral_angle_1_deg 5.359 r_scangle_it 2.056 r_scbond_it 1.341 r_angle_refined_deg 1.143 r_mcangle_it 0.792 r_mcbond_it 0.471 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.871 r_dihedral_angle_4_deg 15.25 r_dihedral_angle_3_deg 10.656 r_dihedral_angle_1_deg 5.359 r_scangle_it 2.056 r_scbond_it 1.341 r_angle_refined_deg 1.143 r_mcangle_it 0.792 r_mcbond_it 0.471 r_nbtor_refined 0.305 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.122 r_symmetry_hbond_refined 0.112 r_chiral_restr 0.074 r_metal_ion_refined 0.074 r_symmetry_metal_ion_refined 0.032 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 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 2832 Nucleic Acid Atoms Solvent Atoms 611 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection XDS data reduction XDS data scaling CNS phasing