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Human heparanase in complex with inhibitor R3794
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, 0.1M magnesium chloride, 18% PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.53 51.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.769 α = 90 b = 71.519 β = 95.27 c = 79.32 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 2022-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97 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 2.1 46.61 99.7 0.99 10.8 6.4 30450
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 2.16 100 0.42
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 46.61 28924 1499 99.62 0.20141 0.19878 0.2035 0.25256 0.2547 RANDOM 41.776
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] 3.8 1.24 -3.01 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.106 r_dihedral_angle_1_deg 6.947 r_long_range_B_refined 6.835 r_long_range_B_other 6.814 r_scangle_other 5.286 r_mcangle_it 5.278 r_mcangle_other 5.277 r_dihedral_angle_2_deg 4.581 r_mcbond_it 3.782 r_mcbond_other 3.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.106 r_dihedral_angle_1_deg 6.947 r_long_range_B_refined 6.835 r_long_range_B_other 6.814 r_scangle_other 5.286 r_mcangle_it 5.278 r_mcangle_other 5.277 r_dihedral_angle_2_deg 4.581 r_mcbond_it 3.782 r_mcbond_other 3.771 r_scbond_it 3.637 r_scbond_other 3.637 r_angle_refined_deg 1.484 r_angle_other_deg 0.47 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3646 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing