7PRT

Crystal structure of human heparanase in complex with covalent inhibitor CB678


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% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5251.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.808α = 90
b = 71.622β = 94.894
c = 78.739γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.979524DiamondI03

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
11.77899.80.999114.156984
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)
11.71.730.748

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5e981.752.95156910280099.7070.1940.19150.235938.659
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]
3.6393.175-2.883-1.281
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.159
r_dihedral_angle_4_deg14.926
r_dihedral_angle_3_deg14.795
r_lrange_other7.152
r_lrange_it7.144
r_dihedral_angle_1_deg6.905
r_scangle_other5.599
r_scangle_it5.598
r_mcangle_it4.156
r_mcangle_other4.155
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.159
r_dihedral_angle_4_deg14.926
r_dihedral_angle_3_deg14.795
r_lrange_other7.152
r_lrange_it7.144
r_dihedral_angle_1_deg6.905
r_scangle_other5.599
r_scangle_it5.598
r_mcangle_it4.156
r_mcangle_other4.155
r_scbond_other3.728
r_scbond_it3.726
r_mcbond_it2.993
r_mcbond_other2.993
r_angle_refined_deg1.593
r_angle_other_deg1.299
r_nbd_other0.233
r_nbd_refined0.214
r_symmetry_nbd_refined0.203
r_symmetry_xyhbond_nbd_refined0.202
r_symmetry_nbd_other0.18
r_nbtor_refined0.166
r_xyhbond_nbd_refined0.132
r_symmetry_nbtor_other0.084
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3628
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms117

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing