8B0B | pdb_00008b0b

Crystal structure of human heparanase in complex with covalent inhibitor VB151


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3647.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.442α = 90
b = 70.846β = 98.702
c = 78.293γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976284DiamondI03

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
11.9552.3121000.9894.35.835113
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)
11.9520.621

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5e981.9552.31235090171199.9460.2350.23220.240.29080.2936.986
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]
2.0181.173-3.7581.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.386
r_dihedral_angle_4_deg19.31
r_dihedral_angle_3_deg16.745
r_dihedral_angle_1_deg8.018
r_lrange_it7.085
r_lrange_other7.076
r_scangle_it5.197
r_scangle_other5.196
r_mcangle_it4.322
r_mcangle_other4.321
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3592
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing