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Crystal structure of Multi-functional Polysaccharide lyase Smlt1473 from Stenotrophomonas maltophilia (strain K279a) in apo form at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298.15 0.2M lithium sulfate monohydrate, 0.1M Tris-HCl pH-8.5, 30% (w/v) PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.17 42.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.022 α = 90 b = 66.804 β = 94.386 c = 103.12 γ = 90
Symmetry Space Group P 1 21 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 HELIOS-MX 2016-03-26 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 2.43 43.89 100 0.1232 0.998 19.97 17.66 22678
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 2.53 100 0.4421 0.948 5.11 11.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1QAZ 2.43 43.854 22476 1033 99.153 0.229 0.2273 0.2737 0.2224 21.892
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] 1.836 -0.475 -1.864 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.583 r_dihedral_angle_4_deg 20.319 r_dihedral_angle_3_deg 14.168 r_dihedral_angle_1_deg 5.532 r_lrange_it 4.589 r_lrange_other 4.546 r_scangle_it 3.403 r_scangle_other 3.396 r_scbond_it 2.88 r_scbond_other 2.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.583 r_dihedral_angle_4_deg 20.319 r_dihedral_angle_3_deg 14.168 r_dihedral_angle_1_deg 5.532 r_lrange_it 4.589 r_lrange_other 4.546 r_scangle_it 3.403 r_scangle_other 3.396 r_scbond_it 2.88 r_scbond_other 2.877 r_mcangle_it 2.643 r_mcangle_other 2.643 r_mcbond_it 1.659 r_mcbond_other 1.659 r_angle_other_deg 1.429 r_angle_refined_deg 1.227 r_nbd_other 0.23 r_symmetry_nbd_other 0.198 r_nbd_refined 0.194 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.136 r_symmetry_xyhbond_nbd_refined 0.123 r_symmetry_nbtor_other 0.079 r_symmetry_nbd_refined 0.075 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4782 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling PHASER phasing Coot model building