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Crystal structure of human heparanase in complex with covalent inhibitor VB151
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.442 α = 90 b = 70.846 β = 98.702 c = 78.293 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 2020-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976284 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.95 52.312 100 0.989 4.3 5.8 35113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 0.621
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 5e98 1.95 52.312 35090 1711 99.946 0.235 0.2322 0.2321 0.2908 0.2911 36.986
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] 2.018 1.173 -3.758 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_4_deg 19.31 r_dihedral_angle_3_deg 16.745 r_dihedral_angle_1_deg 8.018 r_lrange_it 7.085 r_lrange_other 7.076 r_scangle_it 5.197 r_scangle_other 5.196 r_mcangle_it 4.322 r_mcangle_other 4.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_4_deg 19.31 r_dihedral_angle_3_deg 16.745 r_dihedral_angle_1_deg 8.018 r_lrange_it 7.085 r_lrange_other 7.076 r_scangle_it 5.197 r_scangle_other 5.196 r_mcangle_it 4.322 r_mcangle_other 4.321 r_scbond_it 3.351 r_scbond_other 3.35 r_mcbond_other 2.989 r_mcbond_it 2.988 r_angle_refined_deg 1.677 r_angle_other_deg 1.272 r_nbd_other 0.25 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.197 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.17 r_symmetry_nbd_refined 0.167 r_symmetry_xyhbond_nbd_other 0.09 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3592 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing