8OHR

Crystal structure of human heparanase in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E98 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.436α = 90
b = 71.08β = 98.433
c = 78.232γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979499DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.843.99499.10.9938.84.644493
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.840.6061.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.843.99444396222599.20.1820.17980.216429.174
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]
0.3330.543-1.61.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg18.056
r_dihedral_angle_3_deg15.328
r_dihedral_angle_1_deg6.992
r_lrange_it6.691
r_lrange_other6.647
r_scangle_it4.99
r_scangle_other4.99
r_mcangle_it3.566
r_mcangle_other3.565
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg18.056
r_dihedral_angle_3_deg15.328
r_dihedral_angle_1_deg6.992
r_lrange_it6.691
r_lrange_other6.647
r_scangle_it4.99
r_scangle_other4.99
r_mcangle_it3.566
r_mcangle_other3.565
r_scbond_it3.317
r_scbond_other3.315
r_mcbond_it2.489
r_mcbond_other2.469
r_angle_refined_deg1.65
r_angle_other_deg1.366
r_nbd_other0.289
r_symmetry_nbd_refined0.216
r_nbd_refined0.211
r_symmetry_nbd_other0.19
r_symmetry_xyhbond_nbd_refined0.185
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.167
r_symmetry_xyhbond_nbd_other0.134
r_symmetry_nbtor_other0.083
r_chiral_restr0.078
r_chiral_restr_other0.029
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3617
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing