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Crystal structure of human diamine oxidase in complex with the inhibitor berenil
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 2.59 52.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.662 α = 90 b = 94.884 β = 90 c = 196.411 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 210r 2009-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95663 Australian Synchrotron MX1
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 2.09 50 96.7 0.139 10.81 4.7 98904 98904 22.352
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 2.09 2.18 91.8 0.61 2.4 4.4 9282
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 2.09 47.46 98837 93778 5059 96.44 0.17052 0.1684 0.1732 0.20983 0.2123 RANDOM 16.579
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] 0.3 -0.37 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.986 r_dihedral_angle_4_deg 15.731 r_dihedral_angle_3_deg 12.368 r_dihedral_angle_1_deg 6.732 r_scangle_it 2.889 r_scbond_it 1.817 r_angle_refined_deg 1.389 r_mcangle_it 1.168 r_angle_other_deg 0.839 r_mcbond_it 0.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.986 r_dihedral_angle_4_deg 15.731 r_dihedral_angle_3_deg 12.368 r_dihedral_angle_1_deg 6.732 r_scangle_it 2.889 r_scbond_it 1.817 r_angle_refined_deg 1.389 r_mcangle_it 1.168 r_angle_other_deg 0.839 r_mcbond_it 0.629 r_mcbond_other 0.145 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 11362 Nucleic Acid Atoms Solvent Atoms 952 Heterogen Atoms 233
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