8OHW

Crystal structure of heparanase from Burkholderia pseudomallei in complex with siastatin B derived inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7PR9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium citrate pH 5.0, 14% (w/v) PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.5451.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.37α = 90
b = 104.61β = 90
c = 113.71γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.979330DiamondI03

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
11.2761.75899.90.99912.68.2238876
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)
11.271.290.518

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-VALUE1.2761.7582387661217399.870.1610.16030.181517.891
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]
0.3580.171-0.529
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.648
r_dihedral_angle_4_deg15.555
r_dihedral_angle_3_deg12.341
r_dihedral_angle_1_deg6.901
r_lrange_it5.715
r_lrange_other5.477
r_scangle_it4.112
r_scangle_other4.111
r_scbond_it2.815
r_scbond_other2.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.648
r_dihedral_angle_4_deg15.555
r_dihedral_angle_3_deg12.341
r_dihedral_angle_1_deg6.901
r_lrange_it5.715
r_lrange_other5.477
r_scangle_it4.112
r_scangle_other4.111
r_scbond_it2.815
r_scbond_other2.814
r_mcangle_other2.408
r_mcangle_it2.399
r_angle_refined_deg1.911
r_mcbond_it1.656
r_mcbond_other1.634
r_angle_other_deg1.618
r_symmetry_nbd_refined0.234
r_nbd_other0.234
r_nbd_refined0.223
r_symmetry_nbd_other0.184
r_symmetry_xyhbond_nbd_refined0.178
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.156
r_chiral_restr0.102
r_symmetry_nbtor_other0.092
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6276
Nucleic Acid Atoms
Solvent Atoms967
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing