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Crystal structure of Burkholderia pseudomallei heparanase in complex with covalent inhibitor VL166
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 293 0.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.87 α = 90 b = 104.137 β = 90 c = 113.988 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 2019-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 1.34 79.89 98.9 0.058 0.022 0.999 13.4 7.6 210296
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 1.34 1.37 1.215 0.607 0.565 1.1
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 1.34 77.002 209958 10582 98.651 0.177 0.1762 0.1747 0.1989 0.1973 21.494
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] 0.946 -0.041 -0.905
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.298 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 12.485 r_dihedral_angle_1_deg 6.785 r_lrange_it 5.531 r_lrange_other 5.308 r_scangle_it 3.868 r_scangle_other 3.868 r_mcangle_other 2.739 r_mcangle_it 2.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.298 r_dihedral_angle_4_deg 16.709 r_dihedral_angle_3_deg 12.485 r_dihedral_angle_1_deg 6.785 r_lrange_it 5.531 r_lrange_other 5.308 r_scangle_it 3.868 r_scangle_other 3.868 r_mcangle_other 2.739 r_mcangle_it 2.737 r_scbond_it 2.63 r_scbond_other 2.63 r_mcbond_it 1.945 r_mcbond_other 1.933 r_angle_refined_deg 1.807 r_angle_other_deg 1.555 r_nbd_other 0.267 r_symmetry_xyhbond_nbd_refined 0.243 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.179 r_symmetry_nbd_refined 0.178 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.171 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_1 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6282 Nucleic Acid Atoms Solvent Atoms 992 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing