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Crystal structure of human heparanase in complex with HepMer M09S05a
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 [5.5]
0.1 M MgCl2
17% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.99 α = 90 b = 71.06 β = 95.09 c = 78.29 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 2015-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.850 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 1.88 52.52 99.8 0.06 12.1 4.1 40880
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 1.93 1.01
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5e8m 1.88 52.52 40866 2036 99.715 0.18 0.1781 0.1789 0.2172 0.2179 taken from apo 40.236
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] 1.898 2.229 -2.732 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.114 r_dihedral_angle_4_deg 15.807 r_dihedral_angle_3_deg 14.304 r_lrange_it 7.635 r_lrange_other 7.634 r_dihedral_angle_1_deg 6.987 r_scangle_it 5.882 r_scangle_other 5.881 r_mcangle_it 4.48 r_mcangle_other 4.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.114 r_dihedral_angle_4_deg 15.807 r_dihedral_angle_3_deg 14.304 r_lrange_it 7.635 r_lrange_other 7.634 r_dihedral_angle_1_deg 6.987 r_scangle_it 5.882 r_scangle_other 5.881 r_mcangle_it 4.48 r_mcangle_other 4.479 r_scbond_other 3.873 r_scbond_it 3.87 r_mcbond_it 3.192 r_mcbond_other 3.192 r_angle_refined_deg 1.581 r_angle_other_deg 1.277 r_symmetry_nbd_refined 0.269 r_nbd_other 0.243 r_nbd_refined 0.198 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.012 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3643 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing