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Crystal structure of human heparanase in complex with heparin tetrasaccharide dp4
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, 0.1 M MgCl2, 17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.22 α = 90 b = 71.12 β = 95.23 c = 78.6 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 PILATUS 6M 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.73 52.64 99 0.06 11.3 4 52479
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.76 0.1
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 (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 5e8m 1.73 78.27 49793 2675 98.97 0.1741 0.17208 0.1815 0.2105 0.2142 RANDOM 36.573
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] 2.29 0.47 -1.33 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.021 r_dihedral_angle_4_deg 18.288 r_dihedral_angle_3_deg 13.146 r_long_range_B_other 8.342 r_long_range_B_refined 8.338 r_scangle_other 6.611 r_dihedral_angle_1_deg 6.34 r_scbond_it 4.26 r_scbond_other 4.236 r_mcangle_it 4.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.021 r_dihedral_angle_4_deg 18.288 r_dihedral_angle_3_deg 13.146 r_long_range_B_other 8.342 r_long_range_B_refined 8.338 r_scangle_other 6.611 r_dihedral_angle_1_deg 6.34 r_scbond_it 4.26 r_scbond_other 4.236 r_mcangle_it 4.224 r_mcangle_other 4.224 r_mcbond_it 2.859 r_mcbond_other 2.859 r_angle_refined_deg 1.777 r_angle_other_deg 0.997 r_chiral_restr 0.105 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 3643 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling