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Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted 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, SITTING DROP 5.5 293 17% PEG3350
0.1 M MES 5.5
0.1 M MgCl2
200 nL:500 nL protein:drop ratio
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.19 α = 90 b = 71.05 β = 95.2 c = 78.69 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-F 2015-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 1.57 46 99.2 0.048 15.8 4.1 70155
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 1.57 1.61 98.4 0.862 1.7 4
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 1.57 46 66696 3448 99.14 0.1673 0.16593 0.177 0.19334 0.2019 RANDOM 29.93
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] 1.57 0.21 -1.18 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.064 r_dihedral_angle_4_deg 13.68 r_dihedral_angle_3_deg 13.257 r_long_range_B_refined 7.211 r_long_range_B_other 7.211 r_dihedral_angle_1_deg 6.405 r_scangle_other 4.836 r_mcangle_it 3.685 r_mcangle_other 3.684 r_scbond_it 3.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.064 r_dihedral_angle_4_deg 13.68 r_dihedral_angle_3_deg 13.257 r_long_range_B_refined 7.211 r_long_range_B_other 7.211 r_dihedral_angle_1_deg 6.405 r_scangle_other 4.836 r_mcangle_it 3.685 r_mcangle_other 3.684 r_scbond_it 3.099 r_scbond_other 3.098 r_mcbond_it 2.368 r_mcbond_other 2.364 r_angle_refined_deg 1.728 r_angle_other_deg 1.016 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 402 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing