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Structure of an LPMO expressed in E.coli (LsAA9A) at 2.78x10^6 Gy
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 20 mM sodium acetate pH 5.5, 150 mM sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.56 51.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.625 α = 90 b = 48.625 β = 90 c = 109.492 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 100 PIXEL DECTRIS EIGER X 9M 2024-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.8551 ESRF ID30B
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 1.34 48.626 100 0.999 14.5 13.7 56933
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 1.34 1.39 100 0.588 13.7
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 1.34 48.626 56863 2736 99.981 0.149 0.147 0.1482 0.178 0.1801 19.524
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] 0.633 0.633 -1.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.074 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 9.711 r_lrange_it 7.678 r_dihedral_angle_1_deg 6.798 r_lrange_other 6.786 r_scangle_it 3.582 r_scangle_other 3.388 r_scbond_it 2.593 r_scbond_other 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.074 r_dihedral_angle_4_deg 19.148 r_dihedral_angle_3_deg 9.711 r_lrange_it 7.678 r_dihedral_angle_1_deg 6.798 r_lrange_other 6.786 r_scangle_it 3.582 r_scangle_other 3.388 r_scbond_it 2.593 r_scbond_other 2.38 r_mcangle_it 2.12 r_mcangle_other 2.119 r_angle_refined_deg 1.736 r_mcbond_it 1.667 r_angle_other_deg 1.502 r_mcbond_other 1.421 r_nbd_refined 0.216 r_symmetry_nbd_other 0.197 r_nbd_other 0.197 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.158 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.096 r_metal_ion_refined 0.093 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 302 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing