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Crystal structure of human heparanase in complex with HepMer M04S02a
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, HANGING 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 = 45.79 α = 90 b = 71.29 β = 95.06 c = 77.92 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 2015-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 1.63 38.45 99.5 0.05 11.7 4 61989
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.67 1.077 0.625 0.465 1.3 3.8
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 1.63 38.45 61968 3083 99.454 0.171 0.1697 0.1713 0.2063 0.1804 from apo structure 35.312
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] 1.14 0.351 -1.096 -0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.901 r_dihedral_angle_4_deg 14.509 r_dihedral_angle_3_deg 13.778 r_lrange_other 8.205 r_lrange_it 8.2 r_dihedral_angle_1_deg 6.696 r_scangle_it 6.442 r_scangle_other 6.439 r_mcangle_it 4.435 r_mcangle_other 4.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.901 r_dihedral_angle_4_deg 14.509 r_dihedral_angle_3_deg 13.778 r_lrange_other 8.205 r_lrange_it 8.2 r_dihedral_angle_1_deg 6.696 r_scangle_it 6.442 r_scangle_other 6.439 r_mcangle_it 4.435 r_mcangle_other 4.435 r_scbond_other 4.352 r_scbond_it 4.349 r_mcbond_it 3.203 r_mcbond_other 3.194 r_angle_refined_deg 1.748 r_angle_other_deg 1.412 r_nbd_other 0.302 r_symmetry_nbd_refined 0.269 r_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.232 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3686 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing