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Neutron structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WA2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 7.4 289 1.05M potassium-sodium tartrate, 25mM HEPES
Crystal Properties Matthews coefficient Solvent content 3 58.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.548 α = 90 b = 61.779 β = 112.13 c = 92.332 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315r 2016-05-31 M SINGLE WAVELENGTH 2 1 neutron 100 PIXEL DECTRIS PILATUS 6M Ni-Ti supermirror neutron guide Detector: iBIXDetector type: WSF PSD (Wavelength Shift Fiber Position Sensitive Detector) 2015-11-10 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 3.0-5.7 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.14 50 99.4 0.069 0.076 0.029 14.8 5.2 296297 16.56 2 1.72 20.94 87.4 0.1249 4.99 2.6639 203273 16.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.16 0.801 0.95 0.504 0.703 3.5 1 1.16 1.18 0.71 0.841 0.446 0.746 3.5 1 1.18 1.2 0.629 0.746 0.394 0.775 3.5 1 1.2 1.23 0.553 0.654 0.344 0.828 3.5 1 1.23 1.25 0.494 0.584 0.307 0.862 3.5 1 1.25 1.28 0.433 0.511 0.269 0.889 3.6 1 1.28 1.32 0.375 0.443 0.233 0.912 3.6 1 1.32 1.35 0.314 0.371 0.194 0.932 3.6 1 1.35 1.39 0.264 0.311 0.163 0.951 3.6 1 1.39 1.44 0.223 0.263 0.138 0.964 3.6 1 1.44 1.49 0.186 0.22 0.115 0.973 3.6 1 1.49 1.55 0.149 0.176 0.093 0.981 3.5 1 1.55 1.62 0.148 0.163 0.067 0.988 5.6 1 1.62 1.7 0.128 0.138 0.052 0.992 7 1 1.7 1.81 0.104 0.113 0.043 0.994 6.9 1 1.81 1.95 0.085 0.093 0.037 0.994 6.6 1 1.95 2.15 0.081 0.086 0.028 0.996 9.6 1 2.15 2.46 0.071 0.075 0.025 0.996 9.5 1 2.46 3.09 0.063 0.067 0.024 0.996 9.1 1 3.09 50 0.056 0.062 0.027 0.992 6.3
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1.14 45.03 1.33 296105 14805 99.28 0.1684 0.1677 0.1677 0.1815 0.1812 27.8236 NEUTRON DIFFRACTION 1.72 20.951 76237 3813 87.23 0.1815 0.18 0.2095
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 f_dihedral_angle_d 22.036 f_angle_d 1.318 f_chiral_restr 0.102 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4890 Nucleic Acid Atoms Solvent Atoms 2667 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing