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Crystal structure of human heparanase
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 2.54 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.765 α = 90 b = 70.972 β = 94.17 c = 78.948 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 2015-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.920 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 1.75 46.64 100 0.05 12 4.2 49329
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 1.75 1.78 99.8 0.847 1.7 4.1
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 SIRAS THROUGHOUT 1.75 46.64 217940 2647 100 0.16596 0.16411 0.1749 0.19989 0.2045 RANDOM 37.357
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] 3.26 1.55 -2.58 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 13.567 r_dihedral_angle_4_deg 13.188 r_long_range_B_refined 7.27 r_long_range_B_other 7.269 r_dihedral_angle_1_deg 6.389 r_scangle_other 5.68 r_mcangle_it 3.879 r_mcangle_other 3.878 r_scbond_it 3.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.818 r_dihedral_angle_3_deg 13.567 r_dihedral_angle_4_deg 13.188 r_long_range_B_refined 7.27 r_long_range_B_other 7.269 r_dihedral_angle_1_deg 6.389 r_scangle_other 5.68 r_mcangle_it 3.879 r_mcangle_other 3.878 r_scbond_it 3.79 r_scbond_other 3.789 r_mcbond_it 2.859 r_mcbond_other 2.859 r_angle_refined_deg 1.735 r_angle_other_deg 0.987 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 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 249 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling SHELX phasing