8BAC

Crystal structure of human heparanase in complex with competitive inhibitor GD05


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7PRT 

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
2.3948.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.838α = 90
b = 71.188β = 98.375
c = 78.628γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2020-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976254DiamondI03

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
12.0537.67799.60.9936.26.730692
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)
12.052.110.672

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-VALUE7PRT2.0537.67730674148899.5490.2260.22350.267445.913
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]
2.0554.443-5.0891.655
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.534
r_dihedral_angle_3_deg16.241
r_dihedral_angle_4_deg14.252
r_dihedral_angle_1_deg7.408
r_lrange_it6.662
r_lrange_other6.658
r_scangle_other4.932
r_scangle_it4.931
r_mcangle_it4.42
r_mcangle_other4.419
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.534
r_dihedral_angle_3_deg16.241
r_dihedral_angle_4_deg14.252
r_dihedral_angle_1_deg7.408
r_lrange_it6.662
r_lrange_other6.658
r_scangle_other4.932
r_scangle_it4.931
r_mcangle_it4.42
r_mcangle_other4.419
r_scbond_other3.211
r_scbond_it3.21
r_mcbond_it3.092
r_mcbond_other3.09
r_angle_refined_deg1.501
r_angle_other_deg1.261
r_chiral_restr_other0.406
r_symmetry_xyhbond_nbd_refined0.252
r_symmetry_nbd_refined0.224
r_nbd_refined0.205
r_symmetry_nbd_other0.195
r_xyhbond_nbd_refined0.188
r_nbd_other0.185
r_nbtor_refined0.169
r_symmetry_xyhbond_nbd_other0.113
r_symmetry_nbtor_other0.082
r_chiral_restr0.065
r_xyhbond_nbd_other0.057
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3627
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing