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Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor GR109
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.21 α = 90 b = 101.07 β = 90 c = 113.59 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 PIXEL DECTRIS EIGER2 XE 16M 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97933 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.31 66.06 98.5 0.051 0.018 0.999 15.7 8.3 220199
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.31 1.34 1.493 0.534 0.682 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5bwi 1.31 66.06 220106 11043 98.361 0.167 0.1657 0.1639 0.1855 0.1832 22.799
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] 1.858 -0.637 -1.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.701 r_dihedral_angle_4_deg 12.568 r_dihedral_angle_3_deg 12.133 r_dihedral_angle_1_deg 6.809 r_lrange_it 5.616 r_lrange_other 5.342 r_scangle_it 4.305 r_scangle_other 4.304 r_scbond_it 2.878 r_scbond_other 2.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.701 r_dihedral_angle_4_deg 12.568 r_dihedral_angle_3_deg 12.133 r_dihedral_angle_1_deg 6.809 r_lrange_it 5.616 r_lrange_other 5.342 r_scangle_it 4.305 r_scangle_other 4.304 r_scbond_it 2.878 r_scbond_other 2.877 r_mcangle_other 2.484 r_mcangle_it 2.481 r_angle_refined_deg 1.897 r_mcbond_it 1.811 r_mcbond_other 1.802 r_angle_other_deg 1.607 r_nbd_other 0.326 r_chiral_restr 0.293 r_symmetry_nbd_refined 0.283 r_symmetry_xyhbond_nbd_refined 0.254 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_other 0.11 r_symmetry_nbtor_other 0.086 r_ncsr_local_group_1 0.086 r_xyhbond_nbd_other 0.079 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6291 Nucleic Acid Atoms Solvent Atoms 991 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing