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An inactive (D136N and D137N) variant of alpha-1,6-mannanase, GH76A of Salegentibacter sp. HEL1_6 in complex with alpha-1,6-mannotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SHD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 14 % v/v 2-propanol,
30 % v/v Glycerol,
70 mM Sodium acetate pH 4.6,
140 mM Calcium chloride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.311 α = 90 b = 82.774 β = 94.44 c = 49.7 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 PILATUS 6M 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.47 82.77 100 0.083 0.091 0.038 0.997 10.1 5.6 50967
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 100 0.371 0.413 0.179 0.928 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6SHD 1.472 49.551 1.34 50884 2568 99.88 0.1643 0.1624 0.1706 0.1994 0.1998 19.9933
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.399 f_angle_d 0.557 f_chiral_restr 0.061 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2690 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 37
Software Software Software Name Purpose Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing