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X-ray structure of the mutant lys300met of polyamine oxidase from zea mays in complex with spermine
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 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 4.85 74.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.957 α = 90 b = 138.957 β = 90 c = 189.8 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 MARMOSAIC 225 mm CCD 2009-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 3.2 50 100 0.192 9.3 5.6 35410
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) 3.2 3.27 100 0.557 3.2 5.6
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 50 33582 1770 99.8 0.185 0.183 0.1875 0.219 0.2211 RANDOM 24.84
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] 1.57 0.78 1.57 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.876 r_dihedral_angle_3_deg 20.591 r_dihedral_angle_4_deg 16.245 r_dihedral_angle_1_deg 10.15 r_scangle_it 1.964 r_angle_refined_deg 1.253 r_scbond_it 1.122 r_mcangle_it 0.775 r_mcbond_it 0.395 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.876 r_dihedral_angle_3_deg 20.591 r_dihedral_angle_4_deg 16.245 r_dihedral_angle_1_deg 10.15 r_scangle_it 1.964 r_angle_refined_deg 1.253 r_scbond_it 1.122 r_mcangle_it 0.775 r_mcbond_it 0.395 r_chiral_restr 0.081 r_bond_refined_d 0.01 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 7480 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 182
Software Software Software Name Purpose MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling