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Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 (WT) from Stenotrophomonas maltophilia (strain K279a) in apo 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 trihydrate pH 5.0, 30% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.71 54.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.131 α = 90 b = 94.737 β = 90 c = 160.499 γ = 90
Symmetry Space Group P 21 21 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 2017-12-26 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 2.63 47.36 91.2 0.1598 0.988 14.36 10.35 21068
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 2.63 2.73 71.3 0.5177 0.635 2.62 3.86
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 2.63 47.304 21024 1031 91.175 0.227 0.2247 0.2283 0.2719 0.2763 13.07
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] -0.513 1.716 -1.203
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.779 r_dihedral_angle_4_deg 20.289 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_1_deg 5.696 r_lrange_it 2.715 r_lrange_other 2.715 r_angle_refined_deg 1.412 r_mcangle_it 1.358 r_mcangle_other 1.358 r_scangle_it 1.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.779 r_dihedral_angle_4_deg 20.289 r_dihedral_angle_3_deg 16.286 r_dihedral_angle_1_deg 5.696 r_lrange_it 2.715 r_lrange_other 2.715 r_angle_refined_deg 1.412 r_mcangle_it 1.358 r_mcangle_other 1.358 r_scangle_it 1.305 r_scangle_other 1.305 r_angle_other_deg 1.263 r_mcbond_it 0.77 r_mcbond_other 0.767 r_scbond_it 0.74 r_scbond_other 0.74 r_symmetry_xyhbond_nbd_other 0.256 r_symmetry_nbd_other 0.201 r_nbd_refined 0.199 r_symmetry_nbd_refined 0.166 r_nbtor_refined 0.158 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4840 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing