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Structure of Heparinase I from Bacteroides eggerthii in complex with calcium cofactor and delta-UA(1-4)Glc 3, 6, N-Sulphated disaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium acetate pH 5.0, 2 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.80088806 56.1126366
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.59 α = 90 b = 91.563 β = 95.593 c = 73.443 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 XE 16M 2023-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953738 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.715 76.452 90.4 0.165 0.983 7.7 6.7 56421
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.715 1.896 1.045 0.596 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.715 76.452 56418 2859 57.306 0.206 0.2037 0.2049 0.2415 0.2051 19.818
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] 0.061 -0.087 0.019 -0.062
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.643 r_dihedral_angle_6_deg 13.44 r_dihedral_angle_3_deg 11.646 r_dihedral_angle_1_deg 7.579 r_lrange_it 3.318 r_lrange_other 3.181 r_scangle_other 1.451 r_scangle_it 1.45 r_mcangle_it 1.372 r_mcangle_other 1.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.643 r_dihedral_angle_6_deg 13.44 r_dihedral_angle_3_deg 11.646 r_dihedral_angle_1_deg 7.579 r_lrange_it 3.318 r_lrange_other 3.181 r_scangle_other 1.451 r_scangle_it 1.45 r_mcangle_it 1.372 r_mcangle_other 1.372 r_angle_refined_deg 1.202 r_scbond_it 0.844 r_scbond_other 0.831 r_mcbond_it 0.786 r_mcbond_other 0.782 r_angle_other_deg 0.417 r_symmetry_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_refined 0.191 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.17 r_nbd_other 0.149 r_symmetry_xyhbond_nbd_other 0.088 r_dihedral_angle_other_2_deg 0.086 r_ncsr_local_group_1 0.081 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.058 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5888 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing