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Structure of Heparinase II complexed with heparan sulfate degradation disaccharide product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FUQ PDB ENTRY 1FUQ
Crystallization Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.28 α = 90 b = 209.36 β = 90 c = 59.22 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS HTC Osmic mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.35 37.57 98.1 0.134 8.3 4.62 103320 1
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 2.35 2.43 90 0.302 4.4 3.81 9372
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 PDB ENTRY 1FUQ 2.35 37.57 103320 5152 98.03 0.231 0.229 0.2297 0.267 0.2698 RANDOM 24.105
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] -1.26 -0.59 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_4_deg 19.011 r_dihedral_angle_3_deg 16.661 r_dihedral_angle_1_deg 5.787 r_scangle_it 1.801 r_angle_refined_deg 1.554 r_scbond_it 1.15 r_mcangle_it 0.589 r_mcbond_it 0.314 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_4_deg 19.011 r_dihedral_angle_3_deg 16.661 r_dihedral_angle_1_deg 5.787 r_scangle_it 1.801 r_angle_refined_deg 1.554 r_scbond_it 1.15 r_mcangle_it 0.589 r_mcbond_it 0.314 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17931 Nucleic Acid Atoms Solvent Atoms 536 Heterogen Atoms 249
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction MOLREP phasing