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Structure of an LPMO expressed in E.coli (LsAA9A) at 4.89x10^4 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 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.54 α = 90 b = 48.54 β = 90 c = 109.51 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 2024-03-02 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 1.84 44.42 100 0.994 6.29 12.3 21593
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 1.85 1.9 99.7 0.627
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 1.85 44.416 21593 1120 99.944 0.195 0.1924 0.2037 0.2383 0.2408 24.514
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] 0.984 0.984 -1.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.522 r_dihedral_angle_4_deg 13.361 r_dihedral_angle_3_deg 9.878 r_dihedral_angle_1_deg 7.382 r_lrange_other 4.633 r_lrange_it 4.629 r_scangle_it 2.762 r_scangle_other 2.761 r_scbond_it 2.031 r_scbond_other 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.522 r_dihedral_angle_4_deg 13.361 r_dihedral_angle_3_deg 9.878 r_dihedral_angle_1_deg 7.382 r_lrange_other 4.633 r_lrange_it 4.629 r_scangle_it 2.762 r_scangle_other 2.761 r_scbond_it 2.031 r_scbond_other 2.03 r_mcangle_other 1.966 r_mcangle_it 1.965 r_mcbond_it 1.591 r_angle_refined_deg 1.524 r_mcbond_other 1.506 r_angle_other_deg 1.333 r_symmetry_nbd_refined 0.294 r_nbd_other 0.263 r_nbd_refined 0.193 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.066 r_metal_ion_refined 0.028 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1787 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing