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Crystal structure of human heparanase in complex with covalent inhibitor VL166
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.4 α = 90 b = 71.01 β = 95.14 c = 79.23 γ = 90
Symmetry Space Group P 1 21 1
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 1.52 52.78 99.9 0.051 0.028 0.998 12.3 4.1 78665
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 1.52 1.56 100 1.341 0.741 0.479 1.1 4.1
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 5e8m 1.52 46.256 78643 3946 99.816 0.167 0.1656 0.1647 0.1882 0.1864 33.372
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] 1.422 1.186 -0.918 -0.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.727 r_dihedral_angle_4_deg 13.983 r_dihedral_angle_3_deg 12.812 r_lrange_it 7.509 r_lrange_other 7.508 r_dihedral_angle_1_deg 6.805 r_scangle_it 6.141 r_scangle_other 6.14 r_scbond_it 4.111 r_scbond_other 4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.727 r_dihedral_angle_4_deg 13.983 r_dihedral_angle_3_deg 12.812 r_lrange_it 7.509 r_lrange_other 7.508 r_dihedral_angle_1_deg 6.805 r_scangle_it 6.141 r_scangle_other 6.14 r_scbond_it 4.111 r_scbond_other 4.11 r_mcangle_other 3.804 r_mcangle_it 3.803 r_mcbond_it 2.789 r_mcbond_other 2.785 r_angle_refined_deg 1.784 r_angle_other_deg 1.434 r_nbd_other 0.307 r_symmetry_nbd_refined 0.267 r_nbd_refined 0.216 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.141 r_symmetry_xyhbond_nbd_other 0.136 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3643 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing