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Apg mutant enzyme D448N of acarbose hydrolase from human gut flora K. grimontii TD1,complex with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289.15 0.02M Magnesium chloride hexahydrate
0.1M HEPES pH 7.5
22% w/v Poly(acrylic acid sodium salt) 5100
Crystal Properties Matthews coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.645 α = 90 b = 75.645 β = 90 c = 401.935 γ = 120
Symmetry Space Group P 65 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 2025-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
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 1.91 46.84 99.8 0.14 0.995 11.7 10.6 54487 23.74
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 1.91 1.95 100 0.943 0.821 2.4
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.91 46.84 1.33 54313 2739 99.7 0.2106 0.2081 0.2089 0.2575 0.2585 25.61
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 14.3226 f_angle_d 0.9985 f_chiral_restr 0.0714 f_plane_restr 0.01 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4827 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing