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Crystal structure of human diamine oxidase in complex with the inhibitor pentamidine
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 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.455 α = 90 b = 94.69 β = 90 c = 196.279 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 2008-11-05 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) 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 2.149 50 95 0.103 9.903 3 89751 89751 29.96
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) 1 2.149 2.23 87.1 0.336 2.7 2.4 8090
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 2.149 25.84 85093 85093 4554 94.98 0.18359 0.18159 0.1831 0.22093 0.2208 RANDOM 21.017
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] 1.2 -0.94 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.9 r_dihedral_angle_4_deg 13.985 r_dihedral_angle_3_deg 11.793 r_dihedral_angle_1_deg 6.521 r_scangle_it 1.932 r_angle_refined_deg 1.199 r_scbond_it 1.191 r_mcangle_it 0.808 r_angle_other_deg 0.784 r_mcbond_it 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.9 r_dihedral_angle_4_deg 13.985 r_dihedral_angle_3_deg 11.793 r_dihedral_angle_1_deg 6.521 r_scangle_it 1.932 r_angle_refined_deg 1.199 r_scbond_it 1.191 r_mcangle_it 0.808 r_angle_other_deg 0.784 r_mcbond_it 0.431 r_mcbond_other 0.081 r_chiral_restr 0.07 r_bond_refined_d 0.008 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 11354 Nucleic Acid Atoms Solvent Atoms 916 Heterogen Atoms 241
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing