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ManDH5- 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 7 297 0.1M MMT buffer (pH 7.0),30% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.81 0.563
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.648 α = 90 b = 99.256 β = 90 c = 153.284 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-F Focusing optics- Toroidal mirror 2018-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.987 ESRF ID29
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 1.5 49.63 100 0.999 19.6 12.7 1151036 14.9
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 1.5 1.53 99.9 0.918
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 Semet derivative 1.5 49.63 1.34 115096 5961 99.94 0.1451 0.1442 0.1507 0.1609 0.1656 25.81
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 6.9792 f_angle_d 1.0715 f_chiral_restr 0.0632 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4690 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms 118
Software Software Software Name Purpose XDS data scaling PHENIX refinement PHASER phasing Coot model building xia2 data reduction Coot model building xia2 data scaling