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Crystal structure of apo human proheparanase
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 7 293 0.1 M Succinate pH 7.0
17% PEG3350
1:250 dilution seed stock
- Seed stock grown in 0.2M Ammonium Nitrate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.501 α = 90 b = 88.061 β = 90 c = 120.497 γ = 90
Symmetry Space Group P 21 21 21
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 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 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 1.9 46.58 99.7 0.038 28 7.9 43065
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 1.9 1.94 99.5 0.397 5.3 7.9
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 1.9 46.58 40876 2123 99.53 0.18743 0.18536 0.1942 0.22729 0.2333 RANDOM 41.878
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] -0.32 0.63 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 18.871 r_dihedral_angle_3_deg 13.131 r_long_range_B_refined 6.708 r_long_range_B_other 6.707 r_dihedral_angle_1_deg 6.401 r_scangle_other 5.037 r_mcangle_it 3.883 r_mcangle_other 3.883 r_scbond_it 3.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.526 r_dihedral_angle_4_deg 18.871 r_dihedral_angle_3_deg 13.131 r_long_range_B_refined 6.708 r_long_range_B_other 6.707 r_dihedral_angle_1_deg 6.401 r_scangle_other 5.037 r_mcangle_it 3.883 r_mcangle_other 3.883 r_scbond_it 3.259 r_scbond_other 3.259 r_mcbond_it 2.813 r_mcbond_other 2.808 r_angle_refined_deg 1.572 r_angle_other_deg 0.939 r_chiral_restr 0.089 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 4072 Nucleic Acid Atoms Solvent Atoms 218 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing