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Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with actinonin
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 14% PEG-3350, 0.2M zinc acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.56 α = 90 b = 56.47 β = 90 c = 145.95 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 2007-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
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 50 98.9 0.101 13.57 7.7 32412 32049 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 93.2 0.388 5 7 4790
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 2 50 30382 1623 98.79 0.21736 0.21484 0.2255 0.26454 0.2741 RANDOM 26.086
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] 1.34 0.51 -1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.388 r_dihedral_angle_4_deg 23.556 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_1_deg 6.831 r_scangle_it 4.107 r_scbond_it 3.052 r_angle_refined_deg 1.964 r_mcangle_it 1.69 r_mcbond_it 1.214 r_symmetry_hbond_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.388 r_dihedral_angle_4_deg 23.556 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_1_deg 6.831 r_scangle_it 4.107 r_scbond_it 3.052 r_angle_refined_deg 1.964 r_mcangle_it 1.69 r_mcbond_it 1.214 r_symmetry_hbond_refined 0.335 r_symmetry_vdw_refined 0.33 r_nbtor_refined 0.314 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.22 r_chiral_restr 0.113 r_metal_ion_refined 0.105 r_bond_refined_d 0.022 r_symmetry_metal_ion_refined 0.02 r_gen_planes_refined 0.008 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 Atoms Number Protein Atoms 2798 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 63
Software Software Software Name Purpose ADSC data collection CNS refinement REFMAC refinement XDS data reduction XDS data scaling CNS phasing