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Crystal structure of human heparanase in complex with covalent inhibitor CB678
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% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.808 α = 90 b = 71.622 β = 94.894 c = 78.739 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 2020-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.979524 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 1.7 78 99.8 0.999 11 4.1 56984
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 1.7 1.73 0.748
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5e98 1.7 52.951 56910 2800 99.707 0.194 0.1915 0.2359 0.2551 38.659
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] 3.639 3.175 -2.883 -1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.159 r_dihedral_angle_4_deg 14.926 r_dihedral_angle_3_deg 14.795 r_lrange_other 7.152 r_lrange_it 7.144 r_dihedral_angle_1_deg 6.905 r_scangle_other 5.599 r_scangle_it 5.598 r_mcangle_it 4.156 r_mcangle_other 4.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.159 r_dihedral_angle_4_deg 14.926 r_dihedral_angle_3_deg 14.795 r_lrange_other 7.152 r_lrange_it 7.144 r_dihedral_angle_1_deg 6.905 r_scangle_other 5.599 r_scangle_it 5.598 r_mcangle_it 4.156 r_mcangle_other 4.155 r_scbond_other 3.728 r_scbond_it 3.726 r_mcbond_it 2.993 r_mcbond_other 2.993 r_angle_refined_deg 1.593 r_angle_other_deg 1.299 r_nbd_other 0.233 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.202 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.132 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.072 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 3628 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing