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Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe JJB355
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 293 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350, 200:500 nl protein:well ratio
Crystal Properties Matthews coefficient Solvent content 2.49 50.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.43 α = 90 b = 71.26 β = 94.92 c = 78.91 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 PILATUS3 6M 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.88 78.62 98.5 0.097 0.992 10.2 3.9 41184
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 1.88 1.92 99.5 0.579 2.6 3.9
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 1.88 78.62 39085 2080 98.44 0.18138 0.17925 0.1896 0.2217 0.2303 RANDOM 40.063
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] 1.8 0.86 -1.48 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.565 r_dihedral_angle_4_deg 13.198 r_dihedral_angle_3_deg 13.101 r_long_range_B_refined 6.825 r_long_range_B_other 6.824 r_dihedral_angle_1_deg 6.121 r_scangle_other 4.93 r_mcangle_other 3.781 r_mcangle_it 3.78 r_scbond_it 3.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.565 r_dihedral_angle_4_deg 13.198 r_dihedral_angle_3_deg 13.101 r_long_range_B_refined 6.825 r_long_range_B_other 6.824 r_dihedral_angle_1_deg 6.121 r_scangle_other 4.93 r_mcangle_other 3.781 r_mcangle_it 3.78 r_scbond_it 3.144 r_scbond_other 3.144 r_mcbond_it 2.632 r_mcbond_other 2.629 r_angle_refined_deg 1.526 r_angle_other_deg 0.942 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 3634 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing