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Crystal structure of Aspergillus nidulans amine oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W7C PDB ENTRY 1w7c
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 298 0.1M sodium acetate (pH 4.4), 25% w/v PEG 2000 MME, 0.2M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.3 62.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.861 α = 90 b = 179.861 β = 90 c = 148.178 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate OSMIC MIRRORS 2010-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.446 38.44 97.4 0.254 7.1 7.7 44740 44740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.56 82.5 0.815 0.815 7.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1w7c 2.45 38.44 42466 42466 2271 99.69 0.21291 0.21073 0.25409 0.2267 RANDOM 17.405
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] -0.89 -0.89 1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 16.652 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_1_deg 6.256 r_scangle_it 1.357 r_angle_refined_deg 1.047 r_scbond_it 0.8 r_angle_other_deg 0.77 r_mcangle_it 0.532 r_mcbond_it 0.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.333 r_dihedral_angle_4_deg 16.652 r_dihedral_angle_3_deg 14.017 r_dihedral_angle_1_deg 6.256 r_scangle_it 1.357 r_angle_refined_deg 1.047 r_scbond_it 0.8 r_angle_other_deg 0.77 r_mcangle_it 0.532 r_mcbond_it 0.274 r_chiral_restr 0.059 r_mcbond_other 0.041 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 5902 Nucleic Acid Atoms Solvent Atoms 336 Heterogen Atoms 123
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing