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Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A0A147EV52-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M PIPES pH 7.0, 25% (w/v) PEGSH (PEG SMEAR HIGH), 0.1 M rubidium(I) chloride, 0.1 M magnesium(II) formate
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.22 α = 90.17 b = 80.41 β = 94.39 c = 82.96 γ = 106.58
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 CdTe 9M 2023-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.61992 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2 47.29 98.8 0.111 0.995 8.4 4.1 128896 31.55
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 98.7 1.034 0.458 1.5 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 39.91 1.95 128873 2011 98.77 0.2373 0.2365 0.2361 0.2899 0.2859 Random selection
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 6.177 f_angle_d 0.984 f_chiral_restr 0.056 f_plane_restr 0.011 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13760 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing