8OHQ

Crystal structure of human heparanase in complex with competitive inhibitor derrived from siastatin B


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52930.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.4850.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.11α = 90
b = 70.92β = 95.53
c = 78.56γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-05-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.917330DiamondI04

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
11.745.93899.60.99810.81.955285
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)
11.71.730.598

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-VALUE1.745.93855284275699.5660.1760.17430.207728.937
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]
1.3570.28-0.658-0.739
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.795
r_dihedral_angle_3_deg14.453
r_dihedral_angle_4_deg12.75
r_lrange_it7.13
r_lrange_other7.12
r_dihedral_angle_1_deg6.809
r_scangle_it5.372
r_scangle_other5.371
r_mcangle_it3.917
r_mcangle_other3.916
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.795
r_dihedral_angle_3_deg14.453
r_dihedral_angle_4_deg12.75
r_lrange_it7.13
r_lrange_other7.12
r_dihedral_angle_1_deg6.809
r_scangle_it5.372
r_scangle_other5.371
r_mcangle_it3.917
r_mcangle_other3.916
r_scbond_it3.514
r_scbond_other3.514
r_mcbond_it2.607
r_mcbond_other2.607
r_angle_refined_deg1.65
r_angle_other_deg1.478
r_chiral_restr_other0.494
r_symmetry_nbd_refined0.354
r_symmetry_xyhbond_nbd_refined0.259
r_nbd_refined0.21
r_symmetry_nbd_other0.192
r_nbd_other0.192
r_xyhbond_nbd_other0.171
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.142
r_symmetry_nbtor_other0.085
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.005
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3640
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing