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Crystal structure of an AA9 LPMO from Aspergillus nidulans, AnLPMOC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B5Q 4B5Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M sodium thiocyanate
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.9 α = 86.459 b = 64.378 β = 85.54 c = 76.237 γ = 68.208
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 EIGER2 XE 16M 2021-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 2.11 75.96 80.5 0.097 0.986 4.9 2 39040
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.17 0.307 0.779 1.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4B5Q 2.11 75.958 39037 1947 80.409 0.217 0.2135 0.2156 0.273 0.2758 16.227
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] -0.175 -0.061 0.015 0.154 0.02 -0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.641 r_dihedral_angle_4_deg 18.64 r_dihedral_angle_3_deg 13.867 r_dihedral_angle_1_deg 8.649 r_lrange_it 3.455 r_lrange_other 3.449 r_scangle_it 1.888 r_scangle_other 1.888 r_mcangle_it 1.88 r_mcangle_other 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.641 r_dihedral_angle_4_deg 18.64 r_dihedral_angle_3_deg 13.867 r_dihedral_angle_1_deg 8.649 r_lrange_it 3.455 r_lrange_other 3.449 r_scangle_it 1.888 r_scangle_other 1.888 r_mcangle_it 1.88 r_mcangle_other 1.88 r_angle_refined_deg 1.728 r_angle_other_deg 1.264 r_mcbond_it 1.141 r_mcbond_other 1.141 r_scbond_it 1.132 r_scbond_other 1.132 r_nbd_other 0.289 r_symmetry_nbd_refined 0.245 r_nbd_refined 0.195 r_symmetry_nbd_other 0.19 r_symmetry_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.167 r_metal_ion_refined 0.126 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.054 r_bond_refined_d 0.008 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 6296 Nucleic Acid Atoms Solvent Atoms 262 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing