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Crystal structure of the N-terminal of an alpha-amylase family glycosyl hydrolase from Vibrio parahaemolyticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.2 M Ammonium sulfate
0.1 M BIS-TRIS pH 5.5
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.67 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.77 α = 90 b = 118.77 β = 90 c = 107.93 γ = 90
Symmetry Space Group P 41 21 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 EIGER X 16M 2025-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL10U2 0.979183 SSRF BL10U2
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 1.96 24.06 99.9 0.989 6 24.6 55878
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 1.96 2.01 0.327
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 1.96 24.06 53037 2775 99.91 0.20051 0.1982 0.2077 0.24588 0.2557 RANDOM 27.39
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] -0.43 -0.43 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.266 r_dihedral_angle_2_deg 9.065 r_dihedral_angle_1_deg 6.822 r_long_range_B_refined 5.057 r_long_range_B_other 5.026 r_scangle_other 4.237 r_scbond_it 2.784 r_scbond_other 2.783 r_mcangle_it 2.772 r_mcangle_other 2.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.266 r_dihedral_angle_2_deg 9.065 r_dihedral_angle_1_deg 6.822 r_long_range_B_refined 5.057 r_long_range_B_other 5.026 r_scangle_other 4.237 r_scbond_it 2.784 r_scbond_other 2.783 r_mcangle_it 2.772 r_mcangle_other 2.772 r_mcbond_it 2.022 r_mcbond_other 2.022 r_angle_refined_deg 1.57 r_angle_other_deg 0.533 r_chiral_restr 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5014 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement Aimless data scaling xia2 data reduction PHENIX phasing PDB_EXTRACT data extraction