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Structure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6- alpha-manno-cyclophellitol carbasugar-stabilised trisaccharide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D4A 4D4A.PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 PEG 3350, ammonium nitrate
Crystal Properties Matthews coefficient Solvent content 1.92 36.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.373 α = 93.61 b = 51.087 β = 92.36 c = 66.198 γ = 98.21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 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 1.35 50.49 95.1 0.026 0.977 14.1 3.5 127986
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 1.35 1.37 88.5 0.398 0.638 3
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.PDB 1.35 50.49 121581 6308 95.03 0.1355 0.1333 0.1318 0.178 0.1751 RANDOM 16.658
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] -0.45 0.35 -0.26 -0.04 -0.12 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.35 r_dihedral_angle_4_deg 25.754 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 6.246 r_rigid_bond_restr 3.479 r_angle_refined_deg 1.867 r_angle_other_deg 1.726 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.35 r_dihedral_angle_4_deg 25.754 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 6.246 r_rigid_bond_restr 3.479 r_angle_refined_deg 1.867 r_angle_other_deg 1.726 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5368 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling MOLREP phasing