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Crystal structure of copper amine oxidase-1 from Hansenula polymorpha in complex with ethylamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EV5 PDB ENTRY 4EV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 8% PEG8000, 0.22 M potassium phosphate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.408 α = 90 b = 232.834 β = 96.66 c = 105.119 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD 2010-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 2.18 50 100 0.108 10 3.8 257277 257277 5
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 2.18 2.22 100 0.457 1.7 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4EV5 2.18 48.97 244276 244276 12922 99.49 0.1528 0.1528 0.15024 0.20129 0.2055 RANDOM 33.281
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 18.835 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_1_deg 8.114 r_scangle_it 4.931 r_scbond_it 3.323 r_mcangle_it 1.909 r_angle_refined_deg 1.594 r_mcbond_it 1.116 r_chiral_restr 0.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.74 r_dihedral_angle_4_deg 18.835 r_dihedral_angle_3_deg 15.73 r_dihedral_angle_1_deg 8.114 r_scangle_it 4.931 r_scbond_it 3.323 r_mcangle_it 1.909 r_angle_refined_deg 1.594 r_mcbond_it 1.116 r_chiral_restr 0.127 r_bond_refined_d 0.016 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31123 Nucleic Acid Atoms Solvent Atoms 3326 Heterogen Atoms 223
Software Software Software Name Purpose HKL-2000 data collection DF model building REFMAC refinement DENZO data reduction SCALEPACK data scaling DF phasing