7PR8

Crystal structure of human heparanase in complex with covalent inhibitor GR109


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5E8M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5351.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.49α = 90
b = 71.29β = 95.2
c = 79.07γ = 90
Symmetry
Space GroupP 1 21 1

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 I030.97933DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.6639.3798.60.0520.0290.99912.54.259928
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.71.4150.7890.5321

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-VALUE5e8m1.6639.3759921302798.5790.1680.16660.194336.497
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]
2.6111.759-2.022-0.894
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.121
r_dihedral_angle_3_deg12.135
r_dihedral_angle_4_deg11.093
r_lrange_it7.606
r_lrange_other7.606
r_dihedral_angle_1_deg6.809
r_scangle_it6.087
r_scangle_other6.086
r_scbond_it4.095
r_scbond_other4.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.121
r_dihedral_angle_3_deg12.135
r_dihedral_angle_4_deg11.093
r_lrange_it7.606
r_lrange_other7.606
r_dihedral_angle_1_deg6.809
r_scangle_it6.087
r_scangle_other6.086
r_scbond_it4.095
r_scbond_other4.094
r_mcangle_other3.933
r_mcangle_it3.932
r_mcbond_it2.921
r_mcbond_other2.917
r_angle_refined_deg1.694
r_angle_other_deg1.375
r_chiral_restr0.28
r_nbd_other0.248
r_symmetry_xyhbond_nbd_refined0.217
r_nbd_refined0.205
r_symmetry_nbd_other0.178
r_symmetry_nbd_refined0.175
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.159
r_symmetry_nbtor_other0.087
r_symmetry_xyhbond_nbd_other0.04
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3643
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing