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Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in ManA bound form at pH-7.0
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 7 298.15 0.2M LiSo4 Monohydrate, 0.1M Sodium Cacodylate pH-7.0, 30%(w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.55 51.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.139 α = 90 b = 160.228 β = 90 c = 46.878 γ = 90
Symmetry Space Group P 21 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 CMOS BRUKER PHOTON 100 2018-04-07 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 2.43 35.76 94.8 0.1 0.993 20.24 12.8 13632
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 2.43 2.53 76.7 0.5379 0.338 1.99 2.47
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 2.43 35.723 13528 620 94.37 0.23 0.2286 0.2312 0.2669 0.2702 32.248
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] 0.316 0.123 -0.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.217 r_dihedral_angle_4_deg 23.111 r_dihedral_angle_3_deg 18.79 r_dihedral_angle_1_deg 5.498 r_lrange_it 4.577 r_lrange_other 4.569 r_mcangle_it 2.991 r_mcangle_other 2.99 r_scangle_it 2.767 r_scangle_other 2.761
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.217 r_dihedral_angle_4_deg 23.111 r_dihedral_angle_3_deg 18.79 r_dihedral_angle_1_deg 5.498 r_lrange_it 4.577 r_lrange_other 4.569 r_mcangle_it 2.991 r_mcangle_other 2.99 r_scangle_it 2.767 r_scangle_other 2.761 r_mcbond_it 1.873 r_mcbond_other 1.87 r_scbond_it 1.735 r_scbond_other 1.717 r_angle_refined_deg 1.504 r_angle_other_deg 1.47 r_nbd_other 0.241 r_symmetry_nbd_other 0.21 r_nbd_refined 0.192 r_nbtor_refined 0.165 r_symmetry_nbd_refined 0.156 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.094 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.022 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2414 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing