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Crystal structure of human diamine oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C10 The starting model for molecular replacement was a partially refined model of the human diamine oxidase we had previously solved in C2221, this was solved using pdb code 2C10 as a starting model.
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 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.506 α = 90 b = 94.784 β = 90 c = 196.525 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 1.799 50 99 0.084 20.034 6.4 158683 158683 16.449
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 1.799 1.86 95.1 0.436 3.7 5.2 15090
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 (All) 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 MOLECULAR REPLACEMENT THROUGHOUT The starting model for molecular replacement was a partially refined model of the human diamine oxidase we had previously solved in C2221, this was solved using pdb code 2C10 as a starting model. 1.799 46.57 158462 150455 8007 98.82 0.16205 0.16205 0.16062 0.1671 0.1889 0.1933 RANDOM 13.537
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] 0.41 -0.15 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.359 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 6.78 r_scangle_it 2.859 r_scbond_it 1.817 r_angle_refined_deg 1.345 r_mcangle_it 1.187 r_angle_other_deg 0.833 r_mcbond_it 0.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.359 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 6.78 r_scangle_it 2.859 r_scbond_it 1.817 r_angle_refined_deg 1.345 r_mcangle_it 1.187 r_angle_other_deg 0.833 r_mcbond_it 0.665 r_mcbond_other 0.172 r_chiral_restr 0.082 r_bond_refined_d 0.011 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 1136 Heterogen Atoms 221
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 PHASER phasing