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Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OJZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 protein solution of 11.3 mg.ml-1 concentration. Drops of 2 micro-l volume of this protein solution were mixed with 1 micro-l of crystallization solution that contained 2.1 M DL-Malic acid pH 7.0, and equilibrated against a reservoir containing 500 micro-l.
Crystal Properties Matthews coefficient Solvent content 3.91 68.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.39 α = 90 b = 163.39 β = 90 c = 166.73 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 100K-M 2016-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.42 43.7 99.9 0.105 0.998 4.74 5.66 444259
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.47 99.9 0.84 0.183 0.656 5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OJZ 1.42 43.7 444242 23668 99.78 0.1616 0.1611 0.1646 0.1704 0.1738 RANDOM 18.766
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 15.645 r_dihedral_angle_3_deg 12.223 r_dihedral_angle_1_deg 5.962 r_angle_refined_deg 1.231 r_angle_other_deg 0.912 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.087 r_dihedral_angle_4_deg 15.645 r_dihedral_angle_3_deg 12.223 r_dihedral_angle_1_deg 5.962 r_angle_refined_deg 1.231 r_angle_other_deg 0.912 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11637 Nucleic Acid Atoms Solvent Atoms 1326 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction