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Structure of an LPMO expressed in E.coli (LsAA9A) at 4.60x10^4 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 2.56 51.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.691 α = 90 b = 48.691 β = 90 c = 109.137 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 2.22 48.691 100 0.985 2.4 11.5 12572
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 2.22 2.3 99.9 0.628
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 2.22 48.691 12542 630 99.888 0.216 0.2153 0.2206 0.2366 0.2433 34.254
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] 0.033 0.033 -0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 15.967 r_dihedral_angle_3_deg 12.495 r_dihedral_angle_1_deg 7.844 r_lrange_other 7.223 r_lrange_it 7.221 r_scangle_it 4.205 r_scangle_other 4.203 r_mcangle_other 3.567 r_mcangle_it 3.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.374 r_dihedral_angle_4_deg 15.967 r_dihedral_angle_3_deg 12.495 r_dihedral_angle_1_deg 7.844 r_lrange_other 7.223 r_lrange_it 7.221 r_scangle_it 4.205 r_scangle_other 4.203 r_mcangle_other 3.567 r_mcangle_it 3.565 r_scbond_it 3.353 r_scbond_other 3.351 r_mcbond_it 2.445 r_mcbond_other 2.291 r_angle_refined_deg 1.514 r_angle_other_deg 1.224 r_nbd_other 0.212 r_symmetry_nbd_other 0.198 r_nbd_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.165 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.164 r_symmetry_nbd_refined 0.159 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.059 r_metal_ion_refined 0.031 r_bond_refined_d 0.007 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 128 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing