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High resolution X-ray structure of E. coli expressed Lentinus similis LPMO.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PQR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 0.1 M citric acid pH 3.5 and 3.0 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.59 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.659 α = 90 b = 48.659 β = 90 c = 109.593 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 2021-04-15 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) Rrim 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 1.09 48.5 91.3 0.059 0.99 19.3 11.99 96541
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 1.09 1.16 0.73
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 7PQR 1.093 48.5 96076 4828 91.614 0.124 0.1235 0.1253 0.1393 0.1402 17.228
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] 0.445 0.445 -0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.202 r_dihedral_angle_4_deg 18.481 r_dihedral_angle_3_deg 9.173 r_dihedral_angle_1_deg 6.835 r_rigid_bond_restr 6.045 r_lrange_it 3.441 r_lrange_other 3.305 r_scbond_it 3.121 r_scbond_other 3.103 r_mcangle_other 2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.202 r_dihedral_angle_4_deg 18.481 r_dihedral_angle_3_deg 9.173 r_dihedral_angle_1_deg 6.835 r_rigid_bond_restr 6.045 r_lrange_it 3.441 r_lrange_other 3.305 r_scbond_it 3.121 r_scbond_other 3.103 r_mcangle_other 2.88 r_scangle_it 2.831 r_mcangle_it 2.814 r_scangle_other 2.795 r_mcbond_it 2.426 r_mcbond_other 2.287 r_angle_refined_deg 2.032 r_angle_other_deg 1.662 r_nbd_other 0.288 r_symmetry_nbd_refined 0.252 r_nbd_refined 0.234 r_symmetry_xyhbond_nbd_refined 0.217 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.139 r_metal_ion_refined 0.111 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.007 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1787 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing