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Crystal structure of human heparanase in complex with covalent inhibitor VB158
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 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.976 α = 90 b = 71.441 β = 95.45 c = 78.261 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 X 16M 2021-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9762 Diamond I04
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 2.1 52.71 100 0.998 8.3 5.7 29584
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 2.1 2.16 0.592 0.8
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 2.1 52.71 29568 1439 99.929 0.204 0.2015 0.2061 0.2621 0.2621 47.328
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] 2.149 2.116 -2.335 -0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_3_deg 16.471 r_dihedral_angle_4_deg 13.176 r_lrange_other 7.987 r_lrange_it 7.984 r_dihedral_angle_1_deg 7.72 r_scangle_other 6.388 r_scangle_it 6.387 r_mcangle_it 5.576 r_mcangle_other 5.576
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.842 r_dihedral_angle_3_deg 16.471 r_dihedral_angle_4_deg 13.176 r_lrange_other 7.987 r_lrange_it 7.984 r_dihedral_angle_1_deg 7.72 r_scangle_other 6.388 r_scangle_it 6.387 r_mcangle_it 5.576 r_mcangle_other 5.576 r_scbond_other 4.394 r_scbond_it 4.392 r_mcbond_it 4.077 r_mcbond_other 4.075 r_angle_refined_deg 1.668 r_angle_other_deg 1.262 r_nbd_other 0.281 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.217 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.09 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.069 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 3610 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing