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Crystal structure of Multi-functional Polysaccharide lyase Smlt1473-H168A from Stenotrophomonas maltophilia (strain K279a) 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 trihdyrate pH-5.0 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.564 α = 90 b = 75.564 β = 90 c = 112.36 γ = 120
Symmetry Space Group P 31 2 1
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 2018-12-23 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 2.6 65.44 96.4 0.114 0.996 16.59 10.07 11515
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 2.6 2.7 78.3 0.3313 0.909 4.25
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 2.6 65.309 11451 515 96.389 0.189 0.1873 0.1953 0.2316 0.2337 20.782
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] -0.272 -0.136 -0.272 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.998 r_dihedral_angle_4_deg 21.006 r_dihedral_angle_3_deg 15.381 r_dihedral_angle_1_deg 6.399 r_lrange_it 4.441 r_lrange_other 4.424 r_scangle_other 2.74 r_scangle_it 2.735 r_mcangle_other 2.438 r_mcangle_it 2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.998 r_dihedral_angle_4_deg 21.006 r_dihedral_angle_3_deg 15.381 r_dihedral_angle_1_deg 6.399 r_lrange_it 4.441 r_lrange_other 4.424 r_scangle_other 2.74 r_scangle_it 2.735 r_mcangle_other 2.438 r_mcangle_it 2.43 r_scbond_it 1.653 r_scbond_other 1.646 r_angle_refined_deg 1.568 r_mcbond_it 1.471 r_mcbond_other 1.437 r_angle_other_deg 1.319 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.212 r_nbd_other 0.192 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.147 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_refined 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2402 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing