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Crystal structure of the catalytic domain of a multi-domain alginate lyase Dp0100 from thermophilic bacterium Defluviitalea phaphyphila
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 298 15% PEG 6000, 0.1 M magnesium acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 261.38 α = 90 b = 261.38 β = 90 c = 58.45 γ = 120
Symmetry Space Group P 3 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 CCD ADSC QUANTUM 1 2018-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 2.85 226.36 100 0.238 0.072 11.5 11.1 53459 67.276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 100 2.036 0.648 1 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.85 62.86 53457 2701 99.936 0.208 0.2071 0.215 0.2233 0.2265 RANDOM 68.494
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] -3.895 -1.947 -3.895 12.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.174 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 7.383 r_lrange_it 4.833 r_lrange_other 4.833 r_mcangle_it 3.194 r_mcangle_other 3.194 r_scangle_it 2.827 r_scangle_other 2.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.174 r_dihedral_angle_4_deg 18.476 r_dihedral_angle_3_deg 14.059 r_dihedral_angle_1_deg 7.383 r_lrange_it 4.833 r_lrange_other 4.833 r_mcangle_it 3.194 r_mcangle_other 3.194 r_scangle_it 2.827 r_scangle_other 2.827 r_mcbond_it 1.895 r_mcbond_other 1.893 r_scbond_other 1.604 r_scbond_it 1.603 r_angle_refined_deg 1.325 r_angle_other_deg 1.153 r_symmetry_xyhbond_nbd_refined 0.282 r_nbd_other 0.227 r_nbd_refined 0.195 r_metal_ion_refined 0.181 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.156 r_symmetry_nbd_refined 0.12 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.049 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6235 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing SHELX phasing PDB_EXTRACT data extraction xia2 data reduction