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Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in ManA bound form at pH-5.0
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 5 298.15 0.2M LiSo4 Monohydrate, 0.1M Sodium acetate pH-5.0, 30% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.89 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.757 α = 90 b = 160.662 β = 90 c = 48.16 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 CMOS BRUKER PHOTON 100 2018-05-13 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 2.31 29.45 95.8 0.155 0.989 10.04 6.39 17710
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 2.31 2.41 80.9 0.5597 0.578 2.14 2.88
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 7FHU 2.31 29.402 17692 892 95.726 0.207 0.2049 0.2083 0.2515 0.2542 20.624
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] 0.726 -1.397 0.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.332 r_dihedral_angle_4_deg 21.311 r_dihedral_angle_3_deg 15.484 r_dihedral_angle_1_deg 5.45 r_lrange_it 4.294 r_lrange_other 4.226 r_scangle_it 2.951 r_scangle_other 2.93 r_angle_other_deg 2.668 r_mcangle_it 2.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.332 r_dihedral_angle_4_deg 21.311 r_dihedral_angle_3_deg 15.484 r_dihedral_angle_1_deg 5.45 r_lrange_it 4.294 r_lrange_other 4.226 r_scangle_it 2.951 r_scangle_other 2.93 r_angle_other_deg 2.668 r_mcangle_it 2.197 r_mcangle_other 2.196 r_scbond_it 1.792 r_scbond_other 1.77 r_angle_refined_deg 1.604 r_mcbond_it 1.362 r_mcbond_other 1.361 r_nbd_other 0.24 r_symmetry_nbd_other 0.222 r_nbd_refined 0.206 r_nbtor_refined 0.164 r_symmetry_nbd_refined 0.157 r_xyhbond_nbd_refined 0.129 r_symmetry_xyhbond_nbd_refined 0.098 r_chiral_restr 0.081 r_symmetry_nbtor_other 0.08 r_bond_other_d 0.035 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2418 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing