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Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) G41M mutant
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 15% PEG-3350, Zinc acetate 100mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.28 α = 90 b = 66.28 β = 90 c = 194.29 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 MARMOSAIC 225 mm CCD 2008-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
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 2.1 50 99.7 0.084 21.56 9.5 26305 26225 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 2.1 2.23 98.2 0.374 6.8 9.5 4082
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 2.1 48.56 24910 1312 100 0.17307 0.17099 0.1719 0.21223 0.2161 RANDOM 22.939
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.653 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_1_deg 5.932 r_scangle_it 4.228 r_scbond_it 2.751 r_angle_refined_deg 1.527 r_mcangle_it 1.47 r_mcbond_it 0.92 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.653 r_dihedral_angle_4_deg 21.449 r_dihedral_angle_3_deg 16.278 r_dihedral_angle_1_deg 5.932 r_scangle_it 4.228 r_scbond_it 2.751 r_angle_refined_deg 1.527 r_mcangle_it 1.47 r_mcbond_it 0.92 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.194 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.119 r_metal_ion_refined 0.105 r_symmetry_metal_ion_refined 0.031 r_bond_refined_d 0.017 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 2856 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 7
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling