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C-terminally truncated dextran dextrinase bound with acarbose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other A preliminary model solved by single-wavelength anomalous dispersion with sulfur atoms.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 10% PEG 6000, 6% Ethylene glycol, 100 mM sodium acetate buffer (pH 3.5)
Crystal Properties Matthews coefficient Solvent content 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.259 α = 90 b = 138.969 β = 90 c = 264.462 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225-HS 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 2.5 49.11 99.9 0.236 0.252 0.99 8.64 7.6 150716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 99.7 1.194 1.202 0.713 7.6
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 49.106 150715 2000 99.918 0.182 0.1819 0.2109 0.1753 34.858
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] 3.744 -1.886 -1.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.72 r_dihedral_angle_4_deg 17.584 r_dihedral_angle_3_deg 12.908 r_dihedral_angle_1_deg 7.084 r_lrange_it 4.365 r_lrange_other 4.328 r_scangle_it 2.945 r_scangle_other 2.945 r_mcangle_other 2.759 r_mcangle_it 2.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.72 r_dihedral_angle_4_deg 17.584 r_dihedral_angle_3_deg 12.908 r_dihedral_angle_1_deg 7.084 r_lrange_it 4.365 r_lrange_other 4.328 r_scangle_it 2.945 r_scangle_other 2.945 r_mcangle_other 2.759 r_mcangle_it 2.758 r_scbond_it 1.839 r_scbond_other 1.839 r_mcbond_it 1.753 r_mcbond_other 1.752 r_angle_refined_deg 1.293 r_angle_other_deg 1.254 r_nbd_other 0.246 r_symmetry_nbd_refined 0.205 r_nbd_refined 0.195 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.158 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.073 r_ncsr_local_group_2 0.064 r_ncsr_local_group_3 0.064 r_ncsr_local_group_1 0.059 r_ncsr_local_group_6 0.057 r_ncsr_local_group_4 0.056 r_ncsr_local_group_5 0.054 r_chiral_restr 0.049 r_symmetry_xyhbond_nbd_other 0.043 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26677 Nucleic Acid Atoms Solvent Atoms 1450 Heterogen Atoms 310
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing