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Structure of an AA16 LPMO-like protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M buffer system 1 (1 M MES/ 1M Imidazole, pH 6.5), 45% EDO_P8K (40% w/v Ethylene glycol, 20% w/v PEG 8000), divalent cations (0.3 M Magnesium Chloride, O.3 M Calcium Chloride)
Crystal Properties Matthews coefficient Solvent content 2.76 55.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.424 α = 90 b = 52.154 β = 105.666 c = 88.855 γ = 90
Symmetry Space Group C 1 2 1
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 4M 2022-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.646 85.554 99.1 0.99 10.5 4 19765
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 2.65 2.69 0.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE Alphafold model 2.646 85.554 19765 967 99.053 0.18 0.1776 0.1844 0.2333 0.2311 50.29
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] 0.11 -0.471 2.542 -2.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.762 r_dihedral_angle_4_deg 22.12 r_dihedral_angle_3_deg 16.87 r_lrange_other 8.816 r_lrange_it 8.813 r_dihedral_angle_1_deg 7.314 r_scangle_it 6.961 r_scangle_other 6.96 r_mcangle_it 5.345 r_mcangle_other 5.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.762 r_dihedral_angle_4_deg 22.12 r_dihedral_angle_3_deg 16.87 r_lrange_other 8.816 r_lrange_it 8.813 r_dihedral_angle_1_deg 7.314 r_scangle_it 6.961 r_scangle_other 6.96 r_mcangle_it 5.345 r_mcangle_other 5.344 r_scbond_it 4.811 r_scbond_other 4.81 r_mcbond_it 3.604 r_mcbond_other 3.591 r_angle_refined_deg 1.66 r_angle_other_deg 1.244 r_nbd_refined 0.199 r_symmetry_nbd_other 0.187 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.17 r_symmetry_nbd_refined 0.162 r_metal_ion_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3815 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 288
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling MOLREP phasing