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Structure of an LPMO expressed in E.coli (LsAA9A) at 2.73x10^6 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 2.5 50.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.081 α = 90 b = 48.081 β = 90 c = 109.052 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 2024-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 1.861 34.022 99.8 0.987 6.3 13.4 20742
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 1.861 1.9 99.6 0.471 13.5
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 1.861 34.022 20454 1055 98.654 0.212 0.21 0.2163 0.2581 0.261 21.029
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] 0.098 0.098 -0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.749 r_dihedral_angle_4_deg 21.268 r_dihedral_angle_3_deg 11.674 r_dihedral_angle_1_deg 7.193 r_lrange_it 5.71 r_lrange_other 5.71 r_scangle_it 2.397 r_scangle_other 2.226 r_mcangle_it 2.03 r_mcangle_other 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.749 r_dihedral_angle_4_deg 21.268 r_dihedral_angle_3_deg 11.674 r_dihedral_angle_1_deg 7.193 r_lrange_it 5.71 r_lrange_other 5.71 r_scangle_it 2.397 r_scangle_other 2.226 r_mcangle_it 2.03 r_mcangle_other 2.03 r_scbond_it 1.702 r_angle_refined_deg 1.532 r_scbond_other 1.407 r_mcbond_it 1.328 r_mcbond_other 1.279 r_angle_other_deg 1.254 r_symmetry_nbd_other 0.187 r_nbd_refined 0.186 r_symmetry_nbd_refined 0.173 r_nbd_other 0.17 r_nbtor_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.062 r_metal_ion_refined 0.048 r_xyhbond_nbd_other 0.036 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 159 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing