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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 Properties Matthews coefficient Solvent content 4.09 69.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 261.324 α = 90 b = 394.812 β = 90 c = 112.187 γ = 90
Symmetry Space Group C 2 2 21
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 0.97179 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.069 98.898 99.5 0.992 11 7.3 348350 32.327
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.069 2.11 0.541 1.1
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) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.069 98.898 348322 17175 99.458 0.223 0.2221 0.2283 0.2402 0.2453 45.922
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] -1.517 -0.122 1.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 16.26 r_dihedral_angle_3_deg 13.36 r_lrange_it 7.91 r_lrange_other 7.91 r_dihedral_angle_1_deg 7.19 r_scangle_it 6.481 r_scangle_other 6.481 r_scbond_it 5.19 r_scbond_other 5.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 16.26 r_dihedral_angle_3_deg 13.36 r_lrange_it 7.91 r_lrange_other 7.91 r_dihedral_angle_1_deg 7.19 r_scangle_it 6.481 r_scangle_other 6.481 r_scbond_it 5.19 r_scbond_other 5.19 r_mcangle_it 4.677 r_mcangle_other 4.677 r_mcbond_it 3.557 r_mcbond_other 3.557 r_angle_refined_deg 1.515 r_angle_other_deg 1.387 r_symmetry_xyhbond_nbd_refined 0.25 r_nbd_other 0.232 r_nbd_refined 0.195 r_metal_ion_refined 0.187 r_symmetry_nbd_other 0.181 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_other 0.153 r_symmetry_xyhbond_nbd_other 0.091 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.074 r_ncsr_local_group_1 0.043 r_ncsr_local_group_2 0.04 r_ncsr_local_group_3 0.04 r_ncsr_local_group_4 0.04 r_ncsr_local_group_5 0.039 r_ncsr_local_group_6 0.038 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21800 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement Aimless data reduction pointless data scaling SHELX phasing