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Structure of an LPMO expressed in E.coli (LsAA9A) at 6.40x10^4 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 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.07 α = 90 b = 48.07 β = 90 c = 108.93 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 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 2.06 48.12 100 0.995 6.63 12.8 15277
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 2.06 2.11 99.8 0.739
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 2.06 48.116 15277 775 99.98 0.19 0.1871 0.1992 0.2396 0.2471 33.493
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] 2.047 2.047 -4.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.854 r_dihedral_angle_4_deg 20.552 r_dihedral_angle_3_deg 11.039 r_dihedral_angle_1_deg 6.776 r_lrange_other 4.487 r_lrange_it 4.485 r_scangle_other 3.44 r_scangle_it 3.427 r_mcangle_it 2.655 r_mcangle_other 2.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.854 r_dihedral_angle_4_deg 20.552 r_dihedral_angle_3_deg 11.039 r_dihedral_angle_1_deg 6.776 r_lrange_other 4.487 r_lrange_it 4.485 r_scangle_other 3.44 r_scangle_it 3.427 r_mcangle_it 2.655 r_mcangle_other 2.654 r_scbond_other 2.476 r_scbond_it 2.474 r_mcbond_it 1.974 r_mcbond_other 1.972 r_angle_refined_deg 1.587 r_angle_other_deg 1.261 r_nbd_other 0.223 r_symmetry_xyhbond_nbd_refined 0.216 r_nbd_refined 0.195 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.186 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.156 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.053 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 152 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing