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Structure of an AA10 Lytic Polysaccharide Monooxygenase from Bacillus amyloliquefaciens with Cu(II) bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 292 0.1 M NaOAc pH 5.0, 20 % PEG-6000, 0.2 M CaCl2
Micro seeded using crystals grown in 0.1 M MMT pH 4.0, 25 % PEG-1500
Crystal Properties Matthews coefficient Solvent content 2.4 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.779 α = 90 b = 73.482 β = 100.4 c = 75.457 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 PIXEL DECTRIS PILATUS 6M-F 2015-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 37.11 99.8 0.142 0.985 5.3 3.3 41043 7.2
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 1.7 1.73 99.4 0.62 1.3 2.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2YOX 1.7 37.11 41020 2062 99.65 0.2249 0.2229 0.23 0.2635 0.2674 RANDOM 9.4268
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] 0.26 -0.42 0.28 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.397 r_dihedral_angle_4_deg 15.785 r_dihedral_angle_3_deg 13.358 r_dihedral_angle_1_deg 6.979 r_angle_other_deg 3.766 r_angle_refined_deg 1.637 r_mcangle_it 1.118 r_mcbond_it 0.664 r_mcbond_other 0.664 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.397 r_dihedral_angle_4_deg 15.785 r_dihedral_angle_3_deg 13.358 r_dihedral_angle_1_deg 6.979 r_angle_other_deg 3.766 r_angle_refined_deg 1.637 r_mcangle_it 1.118 r_mcbond_it 0.664 r_mcbond_other 0.664 r_chiral_restr 0.095 r_gen_planes_other 0.018 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2782 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling REFMAC phasing