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High resolution X-ray structure of Thermoascus aurantiacus LPMO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES pH 7.5, 20m M MgCl2 and 22 %(w/v) polyacrylic acid 5100 sodium salt
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.653 α = 90 b = 89.046 β = 103.335 c = 70.47 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 EIGER X 16M 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9538 MAX IV BioMAX
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 1.06 37.34 84.2 0.054 0.99 18.57 6.6 171807
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 1.06 1.1 0.44 0.89 3.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2YET 1.06 37.37 163069 8758 84.244 0.119 0.11735 0.1201 0.11851 0.119 12.983
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] 0.072 0.194 -0.221 0.052
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.731 r_dihedral_angle_4_deg 20.868 r_dihedral_angle_1_deg 19.132 r_dihedral_angle_3_deg 11.886 r_rigid_bond_restr 8.906 r_lrange_it 3.715 r_scbond_it 3.625 r_scbond_other 3.624 r_lrange_other 3.271 r_scangle_it 3.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.731 r_dihedral_angle_4_deg 20.868 r_dihedral_angle_1_deg 19.132 r_dihedral_angle_3_deg 11.886 r_rigid_bond_restr 8.906 r_lrange_it 3.715 r_scbond_it 3.625 r_scbond_other 3.624 r_lrange_other 3.271 r_scangle_it 3.24 r_scangle_other 3.24 r_angle_refined_deg 2.304 r_mcangle_it 1.834 r_mcangle_other 1.82 r_angle_other_deg 1.624 r_mcbond_it 1.376 r_mcbond_other 1.356 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.203 r_symmetry_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.142 r_chiral_restr 0.129 r_nbd_other 0.103 r_symmetry_nbtor_other 0.1 r_metal_ion_refined 0.091 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_gen_planes_other 0.008 r_bond_other_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3445 Nucleic Acid Atoms Solvent Atoms 719 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction TRUNCATE data scaling REFMAC phasing