5L9Y

Crystal structure of human heparanase, in complex with glucuronic acid configured aziridine probe JJB355


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E8M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350, 200:500 nl protein:well ratio
Crystal Properties
Matthews coefficientSolvent content
2.4950.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.43α = 90
b = 71.26β = 94.92
c = 78.91γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-05-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.8878.6298.50.0970.99210.23.941184
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.9299.50.5792.63.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5E8M1.8878.6239085208098.440.181380.179250.2217RANDOM40.063
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]
1.80.86-1.48-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.565
r_dihedral_angle_4_deg13.198
r_dihedral_angle_3_deg13.101
r_long_range_B_refined6.825
r_long_range_B_other6.824
r_dihedral_angle_1_deg6.121
r_scangle_other4.93
r_mcangle_other3.781
r_mcangle_it3.78
r_scbond_it3.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.565
r_dihedral_angle_4_deg13.198
r_dihedral_angle_3_deg13.101
r_long_range_B_refined6.825
r_long_range_B_other6.824
r_dihedral_angle_1_deg6.121
r_scangle_other4.93
r_mcangle_other3.781
r_mcangle_it3.78
r_scbond_it3.144
r_scbond_other3.144
r_mcbond_it2.632
r_mcbond_other2.629
r_angle_refined_deg1.526
r_angle_other_deg0.942
r_chiral_restr0.093
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3634
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing