7PR7

Crystal structure of human heparanase in complex with covalent inhibitor VL166


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.5251.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.4α = 90
b = 71.01β = 95.14
c = 79.23γ = 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
11.5252.7899.90.0510.0280.99812.34.178665
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)
11.521.561001.3410.7410.4791.14.1

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-VALUE5e8m1.5246.25678643394699.8160.1670.16560.188233.372
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]
1.4221.186-0.918-0.706
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.727
r_dihedral_angle_4_deg13.983
r_dihedral_angle_3_deg12.812
r_lrange_it7.509
r_lrange_other7.508
r_dihedral_angle_1_deg6.805
r_scangle_it6.141
r_scangle_other6.14
r_scbond_it4.111
r_scbond_other4.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.727
r_dihedral_angle_4_deg13.983
r_dihedral_angle_3_deg12.812
r_lrange_it7.509
r_lrange_other7.508
r_dihedral_angle_1_deg6.805
r_scangle_it6.141
r_scangle_other6.14
r_scbond_it4.111
r_scbond_other4.11
r_mcangle_other3.804
r_mcangle_it3.803
r_mcbond_it2.789
r_mcbond_other2.785
r_angle_refined_deg1.784
r_angle_other_deg1.434
r_nbd_other0.307
r_symmetry_nbd_refined0.267
r_nbd_refined0.216
r_symmetry_nbd_other0.186
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.175
r_symmetry_xyhbond_nbd_refined0.141
r_symmetry_xyhbond_nbd_other0.136
r_chiral_restr0.087
r_symmetry_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.011
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 Atoms324
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing