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Catalytic domain from the Aliivibrio salmonicida lytic polysaccharide monooxygenase AsLPMO10B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YN2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293.15 0.1 M phosphate/citrate pH 4.2, 40 % PEG 300
Crystal Properties Matthews coefficient Solvent content 3.41 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.003 α = 90 b = 71.003 β = 90 c = 100.203 γ = 120
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 Kirkpatrick-Baez (KB) mirror pair (VFM, HFM) 2019-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976254 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 33.46 99.9 0.022 0.999 15.3 18.2 62730
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.4 99.7 0.585 0.545 0.9 9.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YN2 1.35 33.46 62414 3085 99.531 0.14 0.1388 0.1624 0.1811 27.772
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] 1.687 0.844 1.687 -5.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.951 r_dihedral_angle_4_deg 15.646 r_dihedral_angle_3_deg 11.894 r_scbond_it 9.175 r_scbond_other 9.171 r_scangle_it 7.092 r_scangle_other 7.089 r_dihedral_angle_1_deg 6.902 r_rigid_bond_restr 5.131 r_lrange_it 4.754
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.951 r_dihedral_angle_4_deg 15.646 r_dihedral_angle_3_deg 11.894 r_scbond_it 9.175 r_scbond_other 9.171 r_scangle_it 7.092 r_scangle_other 7.089 r_dihedral_angle_1_deg 6.902 r_rigid_bond_restr 5.131 r_lrange_it 4.754 r_lrange_other 4.742 r_mcangle_other 3.205 r_mcangle_it 3.176 r_mcbond_it 2.755 r_mcbond_other 2.686 r_angle_refined_deg 1.862 r_angle_other_deg 1.623 r_symmetry_xyhbond_nbd_refined 0.223 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.174 r_nbd_other 0.135 r_metal_ion_refined 0.111 r_chiral_restr 0.103 r_symmetry_nbd_refined 0.102 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement Coot model building