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Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 6.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FHU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298.15 0.2M LiSo4 monohydrate, 0.1M Sodium Cacodylate pH 6.5, 30% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.513 α = 71.326 b = 58.213 β = 89.938 c = 67.543 γ = 74.862
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS BRUKER PHOTON 100 2019-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.54178
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 2.28 53.02 92.3 0.082 0.992 9.17 2.52 26004
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 2.28 2.38 88.2 0.3383 0.753 2.16 1.05
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 7FHU 2.28 53.006 25977 1304 92.209 0.199 0.1962 0.2451 0.2281 17.556
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] 0.849 -0.663 0.152 0.007 -0.203 -1.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.207 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 12.733 r_dihedral_angle_1_deg 5.853 r_lrange_it 3.394 r_lrange_other 3.279 r_scangle_it 2.049 r_scangle_other 2.024 r_mcangle_it 1.731 r_mcangle_other 1.731
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.207 r_dihedral_angle_4_deg 15.156 r_dihedral_angle_3_deg 12.733 r_dihedral_angle_1_deg 5.853 r_lrange_it 3.394 r_lrange_other 3.279 r_scangle_it 2.049 r_scangle_other 2.024 r_mcangle_it 1.731 r_mcangle_other 1.731 r_angle_refined_deg 1.429 r_angle_other_deg 1.294 r_scbond_it 1.268 r_scbond_other 1.24 r_mcbond_it 1.071 r_mcbond_other 1.069 r_symmetry_xyhbond_nbd_other 0.264 r_symmetry_nbd_refined 0.235 r_nbd_refined 0.204 r_symmetry_nbd_other 0.188 r_nbd_other 0.187 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4809 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing