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Crystal structure of the catalytic domain of an AA9 lytic polysaccharide monooxygenase from Thermothelomyces thermophilus (TtLPMO9F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M of sodium formate, 0.02 M ammonium acetate,
0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.84 56.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.891 α = 90 b = 112.293 β = 90 c = 262.381 γ = 90
Symmetry Space Group C 2 2 21
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 2023-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.33 262.38 100 0.324 0.35 0.132 0.993 6.5 13.4 35897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.33 2.41 2.476 2.569 0.681 0.534 14.1
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.33 131.536 35828 1755 99.922 0.164 0.1623 0.1691 0.2041 0.2058 44.215
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] -0.215 -0.786 1.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.689 r_dihedral_angle_3_deg 13.004 r_lrange_it 7.524 r_dihedral_angle_1_deg 7.485 r_lrange_other 7.446 r_dihedral_angle_2_deg 6.454 r_scangle_it 5.92 r_scangle_other 5.92 r_mcangle_it 4.544 r_mcangle_other 4.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.689 r_dihedral_angle_3_deg 13.004 r_lrange_it 7.524 r_dihedral_angle_1_deg 7.485 r_lrange_other 7.446 r_dihedral_angle_2_deg 6.454 r_scangle_it 5.92 r_scangle_other 5.92 r_mcangle_it 4.544 r_mcangle_other 4.544 r_scbond_it 4.173 r_scbond_other 4.172 r_mcbond_it 3.329 r_mcbond_other 3.329 r_angle_refined_deg 1.857 r_angle_other_deg 0.627 r_symmetry_nbd_other 0.21 r_nbd_refined 0.204 r_nbtor_refined 0.182 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.171 r_symmetry_nbd_refined 0.114 r_symmetry_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.087 r_ncsr_local_group_2 0.087 r_ncsr_local_group_3 0.085 r_ncsr_local_group_1 0.08 r_symmetry_xyhbond_nbd_other 0.035 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5085 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing