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Structure of an LPMO expressed in E.coli (LsAA9A) at 7.00x10^4 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 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.885 α = 90 b = 48.885 β = 90 c = 109.648 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 EIGER2 S 16M 2024-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9763 MAX IV BioMAX
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 1.62 48.96 92.6 0.994 7.5 12.9 21896
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 1.62 1.79 71.5 0.744
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 1.624 48.96 21896 1048 67.587 0.166 0.1631 0.1753 0.2171 0.2252 10.95
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] 0.142 0.142 -0.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.691 r_dihedral_angle_4_deg 13.951 r_dihedral_angle_3_deg 11.288 r_dihedral_angle_1_deg 7.086 r_lrange_it 4.424 r_lrange_other 4.205 r_angle_refined_deg 1.532 r_scangle_it 1.397 r_angle_other_deg 1.347 r_scangle_other 1.346
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.691 r_dihedral_angle_4_deg 13.951 r_dihedral_angle_3_deg 11.288 r_dihedral_angle_1_deg 7.086 r_lrange_it 4.424 r_lrange_other 4.205 r_angle_refined_deg 1.532 r_scangle_it 1.397 r_angle_other_deg 1.347 r_scangle_other 1.346 r_mcangle_it 1.002 r_mcangle_other 1.001 r_scbond_it 0.942 r_scbond_other 0.877 r_mcbond_it 0.668 r_mcbond_other 0.627 r_nbd_other 0.289 r_symmetry_nbd_refined 0.285 r_nbd_refined 0.21 r_symmetry_nbd_other 0.193 r_symmetry_xyhbond_nbd_refined 0.184 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.163 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.07 r_metal_ion_refined 0.036 r_bond_refined_d 0.009 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 393 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing