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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 = 261.923 α = 90 b = 261.923 β = 90 c = 58.292 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 2018-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 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 2.759 131.305 100 0.287 0.086 6.2 11 58914 55.997
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 2.76 2.81 99.2 2.497 0.74 0.9 11.2
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 2.759 131.305 58910 2850 99.902 0.2 0.199 0.2069 0.2255 0.2327 RANDOM 60.226
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] -3.17 -1.585 -3.17 10.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.843 r_dihedral_angle_4_deg 16.543 r_dihedral_angle_3_deg 13.357 r_lrange_other 11.788 r_lrange_it 11.78 r_scangle_it 8.55 r_scangle_other 8.549 r_mcangle_other 8.352 r_mcangle_it 8.351 r_dihedral_angle_1_deg 7.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.843 r_dihedral_angle_4_deg 16.543 r_dihedral_angle_3_deg 13.357 r_lrange_other 11.788 r_lrange_it 11.78 r_scangle_it 8.55 r_scangle_other 8.549 r_mcangle_other 8.352 r_mcangle_it 8.351 r_dihedral_angle_1_deg 7.313 r_mcbond_it 5.836 r_mcbond_other 5.823 r_scbond_it 5.694 r_scbond_other 5.694 r_angle_refined_deg 1.284 r_angle_other_deg 1.152 r_nbd_other 0.225 r_symmetry_xyhbond_nbd_refined 0.22 r_metal_ion_refined 0.2 r_nbd_refined 0.193 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.049 r_symmetry_xyhbond_nbd_other 0.014 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6240 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing SHELX phasing xia2 data reduction