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Structural and functional characterization of the bacterial lytic polysaccharide Monooxygenase ScLPMO10D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6IF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 2.0 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.32 62.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.08 α = 90 b = 59.08 β = 90 c = 145.718 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 6M 2016-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97702 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.37 48.57 99.8 0.05 1 22.5 12.6 55188
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.42 99.6 1.369 0.789 1.6 12.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6IF7 1.37 54.81 52497 2712 99.49 0.13045 0.12934 0.1311 0.15232 0.154 RANDOM 23.296
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] 0.09 0.09 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.878 r_dihedral_angle_1_deg 19.067 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_3_deg 11.759 r_long_range_B_refined 9.619 r_rigid_bond_restr 5.253 r_scbond_it 5.165 r_long_range_B_other 4.319 r_scangle_other 4.277 r_scbond_other 4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.878 r_dihedral_angle_1_deg 19.067 r_dihedral_angle_4_deg 15.19 r_dihedral_angle_3_deg 11.759 r_long_range_B_refined 9.619 r_rigid_bond_restr 5.253 r_scbond_it 5.165 r_long_range_B_other 4.319 r_scangle_other 4.277 r_scbond_other 4.01 r_mcangle_it 2.53 r_mcangle_other 2.499 r_mcbond_it 2.122 r_angle_refined_deg 2.104 r_mcbond_other 2.092 r_angle_other_deg 1.684 r_chiral_restr 0.11 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1351 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing