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Crystal structure of GHdex dextranase (BT3087), E360A catalytic mutant with bound IMO3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously solved structure of BT3087 E360A apo used for MR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Co-crystallisation where the protein was pre-incubated with 5mM dextran 1.5 before being dispensed into trays
Condition:
0.5M Lithium chloride
1.6M Ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.68 54.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.224 α = 90 b = 92.224 β = 90 c = 328.033 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 2021-10-15 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 2.2 47.03 100 0.319 0.332 0.09 0.996 7.7 24.8 73184
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) 2.2 2.25 100 2.225 2.397 0.871 0.505 1.1 13.7
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 2.2 46.294 73027 3603 99.947 0.205 0.2017 0.2016 0.2617 0.2617 38.107
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] 1.137 1.137 -2.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.176 r_dihedral_angle_6_deg 13.696 r_lrange_it 11.009 r_scangle_it 8.074 r_dihedral_angle_1_deg 7.27 r_dihedral_angle_2_deg 7.093 r_scbond_it 6.004 r_mcangle_it 4.925 r_mcbond_it 3.658 r_angle_refined_deg 1.885
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.176 r_dihedral_angle_6_deg 13.696 r_lrange_it 11.009 r_scangle_it 8.074 r_dihedral_angle_1_deg 7.27 r_dihedral_angle_2_deg 7.093 r_scbond_it 6.004 r_mcangle_it 4.925 r_mcbond_it 3.658 r_angle_refined_deg 1.885 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.255 r_nbd_refined 0.213 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.124 r_ncsr_local_group_1 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9000 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data collection MOLREP phasing Coot model building