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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 2.57 52.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.727 α = 90 b = 48.727 β = 90 c = 109.319 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 1.7 48.727 100 0.994 6.3 13.4 28034
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 1.7 1.76 100 0.553 11
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 1.7 48.727 27987 1397 99.971 0.185 0.1832 0.1947 0.2233 0.2283 21.089
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] 0.682 0.682 -1.363
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.765 r_dihedral_angle_4_deg 17.641 r_dihedral_angle_3_deg 10.759 r_dihedral_angle_1_deg 7.252 r_lrange_it 5.993 r_lrange_other 5.473 r_scangle_it 3.005 r_scangle_other 2.48 r_scbond_it 2.319 r_mcangle_other 1.852
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.765 r_dihedral_angle_4_deg 17.641 r_dihedral_angle_3_deg 10.759 r_dihedral_angle_1_deg 7.252 r_lrange_it 5.993 r_lrange_other 5.473 r_scangle_it 3.005 r_scangle_other 2.48 r_scbond_it 2.319 r_mcangle_other 1.852 r_mcangle_it 1.851 r_scbond_other 1.844 r_angle_refined_deg 1.52 r_mcbond_it 1.462 r_mcbond_other 1.413 r_angle_other_deg 1.395 r_metal_ion_refined 0.414 r_nbd_other 0.284 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.221 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.041 r_bond_refined_d 0.01 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 348 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling FFT phasing