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Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 5.5
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 5.5 298.15 0.24M LiSo4 monohydrate, 100mM BIS-TRIS, pH5.5, PEG 3350 25%(w/v)
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.272 α = 90 b = 94.668 β = 90 c = 160.408 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 2017-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
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 2.06 49.27 96.2 0.1191 0.996 19.58 15.34 45555
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 2.06 2.16 89.8 0.4337 0.75 3.27 4.35
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 2.061 47.204 45495 2216 96.216 0.209 0.207 0.2141 0.2548 0.2578 13.818
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] -0.395 1.48 -1.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.522 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_1_deg 6.094 r_lrange_it 3.716 r_lrange_other 3.513 r_scangle_it 1.896 r_scangle_other 1.896 r_mcangle_it 1.599 r_mcangle_other 1.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.522 r_dihedral_angle_4_deg 17.37 r_dihedral_angle_3_deg 12.892 r_dihedral_angle_1_deg 6.094 r_lrange_it 3.716 r_lrange_other 3.513 r_scangle_it 1.896 r_scangle_other 1.896 r_mcangle_it 1.599 r_mcangle_other 1.599 r_angle_refined_deg 1.53 r_angle_other_deg 1.369 r_scbond_it 1.189 r_scbond_other 1.189 r_mcbond_it 0.986 r_mcbond_other 0.986 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.213 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.164 r_nbd_other 0.161 r_symmetry_nbd_refined 0.11 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.03 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4848 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing