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Crystal structure of human heparanase in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor
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 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.436 α = 90 b = 71.08 β = 98.433 c = 78.232 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 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 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 1.8 43.994 99.1 0.993 8.8 4.6 44493
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 1.8 1.84 0.606 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 43.994 44396 2225 99.2 0.182 0.1798 0.193 0.2164 0.2268 29.174
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] 0.333 0.543 -1.6 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.976 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 15.328 r_dihedral_angle_1_deg 6.992 r_lrange_it 6.691 r_lrange_other 6.647 r_scangle_it 4.99 r_scangle_other 4.99 r_mcangle_it 3.566 r_mcangle_other 3.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.976 r_dihedral_angle_4_deg 18.056 r_dihedral_angle_3_deg 15.328 r_dihedral_angle_1_deg 6.992 r_lrange_it 6.691 r_lrange_other 6.647 r_scangle_it 4.99 r_scangle_other 4.99 r_mcangle_it 3.566 r_mcangle_other 3.565 r_scbond_it 3.317 r_scbond_other 3.315 r_mcbond_it 2.489 r_mcbond_other 2.469 r_angle_refined_deg 1.65 r_angle_other_deg 1.366 r_nbd_other 0.289 r_symmetry_nbd_refined 0.216 r_nbd_refined 0.211 r_symmetry_nbd_other 0.19 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 r_chiral_restr_other 0.029 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3617 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing