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Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IU7 PDB ENTRY 1IU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 6.8 289 1.05M potassium tartrate, 25mM HEPES (pH6.8), MICRODIALYSIS, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3 59.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.012 α = 90 b = 63.027 β = 111.96 c = 184.119 γ = 90
Symmetry Space Group I 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 Bruker DIP-6040 2003-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.68 50 99.7 0.042 190544 190511 3.7 19.5
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) 1.68 1.74 99.1 0.338 18830
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IU7 1.68 39.88 1 190511 190506 9539 99.4 0.245 0.245 0.1799 0.254 0.199 RANDOM 25.8
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] -6.67 0.65 11.35 -4.68
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.4 c_scangle_it 2.88 c_scbond_it 1.92 c_mcangle_it 1.72 c_angle_deg 1.4 c_mcbond_it 1.13 c_improper_angle_d 0.75 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.4 c_scangle_it 2.88 c_scbond_it 1.92 c_mcangle_it 1.72 c_angle_deg 1.4 c_mcbond_it 1.13 c_improper_angle_d 0.75 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9736 Nucleic Acid Atoms Solvent Atoms 1135 Heterogen Atoms 2
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing