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X-ray structure of the mutant lys300met of polyamine oxidase from zea mays in complex with spermidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 50% SATURATED AMMONIUM SULFATE
SOLUTION, 0.1M SODIUM ACETATE PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.74 74.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.676 α = 90 b = 137.676 β = 90 c = 189.148 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 4 2009-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.933 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.2 46.5 100 0.195 8.6 5 34813 34784 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.2 3.31 100 0.578 3 5.1
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 3KPF 3.2 46.5 32998 1749 99.93 0.19367 0.19247 0.1974 0.21627 0.2193 RANDOM 30.137
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] 1.55 0.77 1.55 -2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.696 r_dihedral_angle_3_deg 17.128 r_dihedral_angle_4_deg 13.418 r_dihedral_angle_1_deg 5.006 r_scangle_it 1.364 r_angle_refined_deg 1.238 r_scbond_it 0.796 r_mcangle_it 0.617 r_mcbond_it 0.321 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.696 r_dihedral_angle_3_deg 17.128 r_dihedral_angle_4_deg 13.418 r_dihedral_angle_1_deg 5.006 r_scangle_it 1.364 r_angle_refined_deg 1.238 r_scbond_it 0.796 r_mcangle_it 0.617 r_mcbond_it 0.321 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined 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 7487 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 174
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling