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ManDH5 E303Q in complex with mannotetraose after co-crystalliztion with mannotetraose at 1.6 angstroms resolution a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 0.1 M MMT buffer, pH 7.15, 27% PEG 1500, 0.01% Na-azide, 12.5mM Mannohexaose (drop ratio of 1:125 enzyme:substrate).
Crystal Properties Matthews coefficient Solvent content 2.84 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.942 α = 90 b = 99.482 β = 90 c = 153.448 γ = 90
Symmetry Space Group I 2 2 2
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 2019-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.83 83.5 99.8 0.998 16.6 13.4 64042 22.79
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 1.83 1.87 99.2 0.715 1.8 13.8
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 FREE R-VALUE Native ManDH5 1.83 51.17 1.33 3247 6288 99.71 0.174 0.1726 0.1741 0.2021 0.2035
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 13.715 f_angle_d 0.879 f_chiral_restr 0.057 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4735 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 118
Software Software Software Name Purpose PHENIX refinement XDS data reduction xia2 data scaling PHASER phasing Coot model building