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Crystal structure of Escherichia coli amine oxidase mutant 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 291.15 1.6 M Sodium citrate, 100mM HEPES pH 6-7
Crystal Properties Matthews coefficient Solvent content 2.78 55.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.521 α = 90 b = 167.202 β = 90 c = 79.939 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 PIXEL DECTRIS PILATUS 6M-F 2012-05-05 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 1.8 72.12 99.31 0.054 0.061 0.027 0.999 14.7 4.9 167221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 95.2 0.666 0.806 2.2 4.9
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 1.8 72.12 161438 5691 99.16 0.16674 0.16567 0.1751 0.1968 0.2047 RANDOM 34.824
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 -2.45 4.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.023 r_dihedral_angle_4_deg 18.261 r_dihedral_angle_3_deg 12.614 r_dihedral_angle_1_deg 6.569 r_long_range_B_refined 6.384 r_long_range_B_other 6.384 r_scangle_other 4.844 r_mcangle_it 3.355 r_mcangle_other 3.355 r_scbond_it 3.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.023 r_dihedral_angle_4_deg 18.261 r_dihedral_angle_3_deg 12.614 r_dihedral_angle_1_deg 6.569 r_long_range_B_refined 6.384 r_long_range_B_other 6.384 r_scangle_other 4.844 r_mcangle_it 3.355 r_mcangle_other 3.355 r_scbond_it 3.083 r_scbond_other 3.082 r_mcbond_it 2.372 r_mcbond_other 2.372 r_angle_refined_deg 1.556 r_angle_other_deg 0.942 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 11343 Nucleic Acid Atoms Solvent Atoms 1113 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing