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Crystal structure of human heparanase in complex with covalent inhibitor GR109
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, HANGING DROP 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.49 α = 90 b = 71.29 β = 95.2 c = 79.07 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 1.66 39.37 98.6 0.052 0.029 0.999 12.5 4.2 59928
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 1.66 1.7 1.415 0.789 0.532 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 1.66 39.37 59921 3027 98.579 0.168 0.1666 0.1661 0.1943 0.1941 36.497
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] 2.611 1.759 -2.022 -0.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.121 r_dihedral_angle_3_deg 12.135 r_dihedral_angle_4_deg 11.093 r_lrange_it 7.606 r_lrange_other 7.606 r_dihedral_angle_1_deg 6.809 r_scangle_it 6.087 r_scangle_other 6.086 r_scbond_it 4.095 r_scbond_other 4.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.121 r_dihedral_angle_3_deg 12.135 r_dihedral_angle_4_deg 11.093 r_lrange_it 7.606 r_lrange_other 7.606 r_dihedral_angle_1_deg 6.809 r_scangle_it 6.087 r_scangle_other 6.086 r_scbond_it 4.095 r_scbond_other 4.094 r_mcangle_other 3.933 r_mcangle_it 3.932 r_mcbond_it 2.921 r_mcbond_other 2.917 r_angle_refined_deg 1.694 r_angle_other_deg 1.375 r_chiral_restr 0.28 r_nbd_other 0.248 r_symmetry_xyhbond_nbd_refined 0.217 r_nbd_refined 0.205 r_symmetry_nbd_other 0.178 r_symmetry_nbd_refined 0.175 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.159 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 308 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling REFMAC phasing