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Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide
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 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.974 α = 90 b = 70.856 β = 97.128 c = 78.455 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 EIGER X 16M 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.68 52.4 91 0.045 0.025 0.999 7.8 4.1 24849
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 1.68 1.951 65.7 0.667 0.371 0.692 1.8
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 1.714 52.4 24830 1206 47.266 0.182 0.1788 0.1789 0.2412 0.2413 39.659
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] 0.18 0.282 -0.527 0.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_4_deg 16.227 r_dihedral_angle_3_deg 14.999 r_dihedral_angle_1_deg 7.579 r_lrange_it 7.573 r_lrange_other 7.416 r_scangle_it 5.085 r_scangle_other 4.979 r_mcangle_it 4.718 r_mcangle_other 4.717
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.828 r_dihedral_angle_4_deg 16.227 r_dihedral_angle_3_deg 14.999 r_dihedral_angle_1_deg 7.579 r_lrange_it 7.573 r_lrange_other 7.416 r_scangle_it 5.085 r_scangle_other 4.979 r_mcangle_it 4.718 r_mcangle_other 4.717 r_scbond_it 3.275 r_scbond_other 3.174 r_mcbond_it 3.107 r_mcbond_other 3.107 r_angle_refined_deg 1.574 r_angle_other_deg 1.205 r_symmetry_xyhbond_nbd_refined 0.297 r_symmetry_nbd_refined 0.296 r_nbd_other 0.253 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.199 r_xyhbond_nbd_other 0.195 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.165 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.032 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3628 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement xia2 data reduction STARANISO data scaling REFMAC phasing