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Crystal structure of Escherichia coli amine oxidase mutant I342F/E573Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 100 mM HEPES, 1.2 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.79 55.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.152 α = 90 b = 166.836 β = 90 c = 79.734 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 2012-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 105.05 99.2 0.036 0.04 0.018 1 21.4 5.1 196242
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 97.06 0.785 0.875 0.379 0.873 2.4 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 FOURIER SYNTHESIS THROUGHOUT 1DYU 1.7 105.05 189466 6714 99.15 0.1673 0.16638 0.1784 0.19326 0.2046 RANDOM 33.255
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] -1.5 -2.57 4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.871 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_3_deg 12.283 r_dihedral_angle_1_deg 6.473 r_long_range_B_refined 5.599 r_long_range_B_other 5.596 r_scangle_other 3.982 r_mcangle_other 2.865 r_mcangle_it 2.864 r_scbond_it 2.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.871 r_dihedral_angle_4_deg 18.488 r_dihedral_angle_3_deg 12.283 r_dihedral_angle_1_deg 6.473 r_long_range_B_refined 5.599 r_long_range_B_other 5.596 r_scangle_other 3.982 r_mcangle_other 2.865 r_mcangle_it 2.864 r_scbond_it 2.505 r_scbond_other 2.5 r_mcbond_it 1.953 r_mcbond_other 1.953 r_angle_refined_deg 1.446 r_angle_other_deg 0.908 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11349 Nucleic Acid Atoms Solvent Atoms 1205 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing