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Crystal structure of PL7 family alginate lyase AlyMc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 2.5 M Ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.58 52.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.44 α = 90 b = 65.013 β = 95.073 c = 82.182 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 PIXEL Bruker PHOTON III 2022-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER X8 PROTEUM 1.34
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 2.1 23.99 99.3 0.979 10.6 5.4 36355
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 2.1 2.16 0.595
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.1 20.149 36317 1789 99.151 0.173 0.1707 0.1709 0.2147 0.215 19.648
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] 0.277 -0.265 -0.734 0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.344 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_1_deg 7.724 r_dihedral_angle_2_deg 6.198 r_lrange_it 5.138 r_scangle_it 3.854 r_scbond_it 2.929 r_mcangle_it 2.672 r_mcbond_it 2.046 r_angle_refined_deg 2.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.344 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_1_deg 7.724 r_dihedral_angle_2_deg 6.198 r_lrange_it 5.138 r_scangle_it 3.854 r_scbond_it 2.929 r_mcangle_it 2.672 r_mcbond_it 2.046 r_angle_refined_deg 2.031 r_nbtor_refined 0.308 r_nbd_refined 0.211 r_symmetry_xyhbond_nbd_refined 0.195 r_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.16 r_chiral_restr 0.136 r_bond_refined_d 0.015 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4215 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling XDS data reduction