5L9Z

Crystal structure of human heparanase nucleophile mutant (E343Q), in complex with unreacted 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 DIFFUSION, SITTING DROP5.529317% PEG3350 0.1 M MES 5.5 0.1 M MgCl2 200 nL:500 nL protein:drop ratio
Crystal Properties
Matthews coefficientSolvent content
2.4950.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.19α = 90
b = 71.05β = 95.2
c = 78.69γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.574699.20.04815.84.170155
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)
11.571.6198.40.8621.74

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 REPLACEMENTTHROUGHOUT5E8M1.574666696344899.140.16730.165930.19334RANDOM29.93
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]
1.570.21-1.18-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.064
r_dihedral_angle_4_deg13.68
r_dihedral_angle_3_deg13.257
r_long_range_B_refined7.211
r_long_range_B_other7.211
r_dihedral_angle_1_deg6.405
r_scangle_other4.836
r_mcangle_it3.685
r_mcangle_other3.684
r_scbond_it3.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.064
r_dihedral_angle_4_deg13.68
r_dihedral_angle_3_deg13.257
r_long_range_B_refined7.211
r_long_range_B_other7.211
r_dihedral_angle_1_deg6.405
r_scangle_other4.836
r_mcangle_it3.685
r_mcangle_other3.684
r_scbond_it3.099
r_scbond_other3.098
r_mcbond_it2.368
r_mcbond_other2.364
r_angle_refined_deg1.728
r_angle_other_deg1.016
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3643
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms111

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing