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Structure of the D125N mutant of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol trisaccharide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG 3350, ammonium nitrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.861 α = 90 b = 66.422 β = 100.13 c = 98.892 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 DECTRIS EIGER2 XE 16M 2020-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.4 54.87 99.4 0.029 0.998 6.7 4.2 109221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 98.6 0.629 0.633 0.9 4.2
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 4D4A 1.4 48.72 103667 5531 99.27 0.1564 0.1536 0.1615 0.2062 0.2105 RANDOM 19.224
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] -0.15 0.9 -0.26 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.66 r_dihedral_angle_4_deg 23.776 r_dihedral_angle_3_deg 12.814 r_dihedral_angle_1_deg 6.337 r_rigid_bond_restr 3.862 r_angle_refined_deg 1.772 r_angle_other_deg 1.648 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.66 r_dihedral_angle_4_deg 23.776 r_dihedral_angle_3_deg 12.814 r_dihedral_angle_1_deg 6.337 r_rigid_bond_restr 3.862 r_angle_refined_deg 1.772 r_angle_other_deg 1.648 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5269 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing