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Apg, crystal structure of acarbose hydrolase from the human gut flora K. grimontii TD1
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 7 289.15 0.02 M magnesium chloride hexahydrate, 0.1 M HEPES (pH 7.0), and 22% w/v poly( acrylic acid sodium salt) 5100
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.798 α = 90 b = 75.798 β = 90 c = 401.78 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 2023-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97852 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 2.32 34.28 100 0.183 0.993 8.2 7.7 31154 28.54
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 2.32 2.4 100 0.898 0.87 2.2 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 7VT9 2.32 34.28 1.34 30986 1550 99.83 0.2072 0.2053 0.2065 0.2432 0.2434 31.88
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 14.6091 f_angle_d 0.8788 f_chiral_restr 0.0521 f_plane_restr 0.0081 f_bond_d 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4846 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing