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Structure of Heparinase I from Bacteroides eggerthii in complex with calcium cofactor
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 2.69 54.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.194 α = 90 b = 91.485 β = 95.46 c = 73.448 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 2022-12-10 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) Rpim I (All) 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 1.85 54.29 99.92 0.387 0.159 0.966 6.4 7 78798
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 1.85 1.88 2.965 1.207 0.351 0.8
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 1.85 54.29 78793 3925 99.914 0.212 0.2103 0.2115 0.2468 0.2487 24.432
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] -0.193 -0.215 0.134 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.949 r_dihedral_angle_3_deg 10.359 r_dihedral_angle_1_deg 7.398 r_dihedral_angle_2_deg 6.973 r_lrange_it 5.372 r_lrange_other 5.13 r_scangle_it 2.507 r_scangle_other 2.34 r_mcangle_it 1.994 r_mcangle_other 1.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 12.949 r_dihedral_angle_3_deg 10.359 r_dihedral_angle_1_deg 7.398 r_dihedral_angle_2_deg 6.973 r_lrange_it 5.372 r_lrange_other 5.13 r_scangle_it 2.507 r_scangle_other 2.34 r_mcangle_it 1.994 r_mcangle_other 1.994 r_scbond_it 1.588 r_scbond_other 1.378 r_angle_refined_deg 1.254 r_mcbond_it 1.2 r_mcbond_other 1.181 r_angle_other_deg 0.446 r_symmetry_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.209 r_nbd_refined 0.2 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.177 r_nbd_other 0.163 r_symmetry_xyhbond_nbd_other 0.113 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.061 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5911 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 177
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing