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Hansenula polymorpha copper amine oxidase-1 in complex with Co(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OOV PDB ID 2OOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 298 8.5% PEG 8000, 0.27 M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.887 α = 90 b = 223.364 β = 95.61 c = 103.969 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 ADSC QUANTUM 315r 2007-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.27 50 94.9 0.073 23.5 3.7 1169541 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.32 85.3 0.357 3.4 3.4
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 FOURIER SYNTHESIS THROUGHOUT PDB ID 2OOV 1.27 31.7 1170625 1110572 58671 94.9 0.109 0.108 0.1074 0.138 0.1376 RANDOM 13.14
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] -0.03 -0.06 0.04 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.193 r_dihedral_angle_4_deg 18.04 r_dihedral_angle_3_deg 11.813 r_dihedral_angle_1_deg 7.853 r_scangle_it 7.414 r_scbond_it 5.477 r_mcangle_it 3.761 r_rigid_bond_restr 3.105 r_mcbond_it 2.744 r_angle_refined_deg 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.193 r_dihedral_angle_4_deg 18.04 r_dihedral_angle_3_deg 11.813 r_dihedral_angle_1_deg 7.853 r_scangle_it 7.414 r_scbond_it 5.477 r_mcangle_it 3.761 r_rigid_bond_restr 3.105 r_mcbond_it 2.744 r_angle_refined_deg 1.89 r_chiral_restr 0.24 r_bond_refined_d 0.019 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31402 Nucleic Acid Atoms Solvent Atoms 6225 Heterogen Atoms 274
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling