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Crystal structure of heparanase from Burkholderia pseudomallei in complex with siastatin B derived inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.54 51.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.37 α = 90 b = 104.61 β = 90 c = 113.71 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 EIGER2 XE 16M 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.979330 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.27 61.758 99.9 0.999 12.6 8.2 238876
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.27 1.29 0.518
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 1.27 61.758 238766 12173 99.87 0.161 0.1603 0.1609 0.1815 0.1821 17.891
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] 0.358 0.171 -0.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_4_deg 15.555 r_dihedral_angle_3_deg 12.341 r_dihedral_angle_1_deg 6.901 r_lrange_it 5.715 r_lrange_other 5.477 r_scangle_it 4.112 r_scangle_other 4.111 r_scbond_it 2.815 r_scbond_other 2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.648 r_dihedral_angle_4_deg 15.555 r_dihedral_angle_3_deg 12.341 r_dihedral_angle_1_deg 6.901 r_lrange_it 5.715 r_lrange_other 5.477 r_scangle_it 4.112 r_scangle_other 4.111 r_scbond_it 2.815 r_scbond_other 2.814 r_mcangle_other 2.408 r_mcangle_it 2.399 r_angle_refined_deg 1.911 r_mcbond_it 1.656 r_mcbond_other 1.634 r_angle_other_deg 1.618 r_symmetry_nbd_refined 0.234 r_nbd_other 0.234 r_nbd_refined 0.223 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6276 Nucleic Acid Atoms Solvent Atoms 967 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing