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AA13 Lytic polysaccharide monooxygenase from Aspergillus oryzae partially in Cu(II) state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 0.1 M buffer system (II) (0.2 M L-malic acid, 0.04 M MES, 0.4 M Tris) pH 5, 0.2 M Zn-acetate, 23% PEG 3000.
The crystals were soaked in 0.09 M Buffer system (II) pH 5, 22.5% PEG 3000, 0.5 M Cu-acetate, 1 mg/ml BSA
Crystal Properties Matthews coefficient Solvent content 2.02 39.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.305 α = 90 b = 61.316 β = 90 c = 72.982 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2017-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.30 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.72 46.9 99.1 0.332 0.987 4.6 3.77 21830
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.76 2.327 0.425 0.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 4OPB 1.72 46.9 21830 778 99.03 0.222 0.2205 0.2633 0.2362 RANDOM 24.441
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] 1.13 -1.93 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.219 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_3_deg 16.578 r_dihedral_angle_1_deg 8.276 r_angle_refined_deg 1.441 r_angle_other_deg 0.977 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.219 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_3_deg 16.578 r_dihedral_angle_1_deg 8.276 r_angle_refined_deg 1.441 r_angle_other_deg 0.977 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1799 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC phasing