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Crystal structure of apo GHdex dextranase (BT3087), wild type
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Used our previously solved BT3087 E360A structure to solve phases
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M MES
0.8-3.2M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.8 56.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.698 α = 90 b = 93.698 β = 90 c = 331.612 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 EIGER2 XE 16M 2021-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.89842 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.8 55.27 100 0.161 0.167 0.046 0.999 13.4 25.1 137723
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.83 100 2.239 2.323 0.618 0.81 1.6 27.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 54.133 137436 6909 99.9 0.2 0.1982 0.1982 0.2291 0.2291 31.862
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] 0.952 0.952 -1.905
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.018 r_dihedral_angle_2_deg 17.941 r_dihedral_angle_6_deg 15.325 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 7.015 r_scangle_it 6.074 r_scbond_it 4.303 r_mcangle_it 3.29 r_mcbond_it 2.627 r_angle_refined_deg 1.815
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 23.018 r_dihedral_angle_2_deg 17.941 r_dihedral_angle_6_deg 15.325 r_dihedral_angle_3_deg 11.967 r_dihedral_angle_1_deg 7.015 r_scangle_it 6.074 r_scbond_it 4.303 r_mcangle_it 3.29 r_mcbond_it 2.627 r_angle_refined_deg 1.815 r_metal_ion_refined 0.589 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.284 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.185 r_chiral_restr 0.132 r_ncsr_local_group_1 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9008 Nucleic Acid Atoms Solvent Atoms 1418 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data collection Coot model building PHASER phasing