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Structure of an LPMO expressed in E.coli (LsAA9A) merged from multiple crystals with an average dose of 1.5 kGy at room temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PYL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 278 25 mM sodium acetate pH 5.5, 20 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.48 α = 90 b = 49.48 β = 90 c = 109.41 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL DECTRIS EIGER X 9M 2024-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE MicroMAX 0.9544 MAX IV MicroMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 49.48 95.8 0.972 3.76 3.52 25358
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.82 97 0.405 3.53
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FOURIER SYNTHESIS FREE R-VALUE 1.75 49.48 25357 1273 95.759 0.168 0.1662 0.1777 0.1916 0.1978 17.338
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] 0.237 0.237 -0.475
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.027 r_dihedral_angle_4_deg 14.594 r_dihedral_angle_3_deg 10.54 r_dihedral_angle_1_deg 6.856 r_lrange_it 4.687 r_lrange_other 4.425 r_scangle_it 2.808 r_scangle_other 2.757 r_scbond_it 1.957 r_mcangle_other 1.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.027 r_dihedral_angle_4_deg 14.594 r_dihedral_angle_3_deg 10.54 r_dihedral_angle_1_deg 6.856 r_lrange_it 4.687 r_lrange_other 4.425 r_scangle_it 2.808 r_scangle_other 2.757 r_scbond_it 1.957 r_mcangle_other 1.818 r_mcangle_it 1.817 r_scbond_other 1.795 r_angle_refined_deg 1.518 r_angle_other_deg 1.356 r_mcbond_it 1.199 r_mcbond_other 1.191 r_nbd_refined 0.194 r_nbd_other 0.194 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.124 r_symmetry_nbd_refined 0.09 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_metal_ion_refined 0.042 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1787 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing