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The structure of human diamine oxidase complexed with an inhibitor aminoguanidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HI7 PDB ENTRY 3HI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M bis-tris propane, 20%(w/v) PEG 3350, 0.2M sodium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.685 α = 90 b = 94.604 β = 90 c = 196.051 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 IMAGE PLATE MAR scanner 345 mm plate OSMIC MIRRORS 2009-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.037 31.136 95.6 0.135 0.135 10.2 4.3 106658 106658 18.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.14 77 0.49 0.49 2.6 3.9 12408
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 BY REFINEMENT THROUGHOUT PDB ENTRY 3HI7 2.05 31.13 106575 101159 5416 97.52 0.1794 0.1775 0.182 0.21486 0.2181 RANDOM 14.103
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] 0.12 -0.34 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.41 r_dihedral_angle_4_deg 16.041 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 6.732 r_scangle_it 2.253 r_scbond_it 1.396 r_angle_refined_deg 1.251 r_mcangle_it 0.928 r_angle_other_deg 0.798 r_mcbond_it 0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.41 r_dihedral_angle_4_deg 16.041 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 6.732 r_scangle_it 2.253 r_scbond_it 1.396 r_angle_refined_deg 1.251 r_mcangle_it 0.928 r_angle_other_deg 0.798 r_mcbond_it 0.496 r_mcbond_other 0.099 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11408 Nucleic Acid Atoms Solvent Atoms 997 Heterogen Atoms 185
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction REFMAC phasing