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Crystal structure of apo GHdex dextranase (BT3087), E360A catalytic mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AXH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 2M ammonium sulphate
0.2M Potassium sodium tartrate
0.1M sodium citrate
pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.74 55.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.862 α = 90 b = 92.862 β = 90 c = 330.684 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 PILATUS3 6M 2021-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97940 Diamond I24
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 2.1 330.68 100 0.892 0.927 0.251 0.99 5.9 25.9 85740
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 17.905 5.021 0.7 1.2 24.7
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 2.1 89.404 85542 4260 99.931 0.192 0.1903 0.1903 0.2295 0.2295 40.846
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] 1.261 1.261 -2.522
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 26.182 r_dihedral_angle_3_deg 14.058 r_dihedral_angle_6_deg 13.806 r_dihedral_angle_2_deg 13.286 r_scangle_it 7.921 r_dihedral_angle_1_deg 7.124 r_scbond_it 5.528 r_mcangle_it 4.28 r_mcbond_it 3.09 r_angle_refined_deg 1.791
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 26.182 r_dihedral_angle_3_deg 14.058 r_dihedral_angle_6_deg 13.806 r_dihedral_angle_2_deg 13.286 r_scangle_it 7.921 r_dihedral_angle_1_deg 7.124 r_scbond_it 5.528 r_mcangle_it 4.28 r_mcbond_it 3.09 r_angle_refined_deg 1.791 r_symmetry_nbd_refined 0.345 r_nbtor_refined 0.311 r_nbd_refined 0.238 r_xyhbond_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.151 r_chiral_restr 0.112 r_ncsr_local_group_1 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9020 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 166
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling DIALS data reduction MrBUMP phasing PARROT phasing Coot model building