6ZDM

Crystal structure of human heparanase in complex with a N',6O'-bis-sulfated 4-methylumbelliferyl heparan sulfate disaccharide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3748.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.974α = 90
b = 70.856β = 97.128
c = 78.455γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.6852.4910.0450.0250.9997.84.124849
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)
11.681.95165.70.6670.3710.6921.8

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-VALUE5e8m1.71452.424830120647.2660.1820.17880.241239.659
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]
0.180.282-0.5270.267
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.828
r_dihedral_angle_4_deg16.227
r_dihedral_angle_3_deg14.999
r_dihedral_angle_1_deg7.579
r_lrange_it7.573
r_lrange_other7.416
r_scangle_it5.085
r_scangle_other4.979
r_mcangle_it4.718
r_mcangle_other4.717
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.828
r_dihedral_angle_4_deg16.227
r_dihedral_angle_3_deg14.999
r_dihedral_angle_1_deg7.579
r_lrange_it7.573
r_lrange_other7.416
r_scangle_it5.085
r_scangle_other4.979
r_mcangle_it4.718
r_mcangle_other4.717
r_scbond_it3.275
r_scbond_other3.174
r_mcbond_it3.107
r_mcbond_other3.107
r_angle_refined_deg1.574
r_angle_other_deg1.205
r_symmetry_xyhbond_nbd_refined0.297
r_symmetry_nbd_refined0.296
r_nbd_other0.253
r_nbd_refined0.209
r_xyhbond_nbd_refined0.199
r_xyhbond_nbd_other0.195
r_symmetry_nbd_other0.185
r_nbtor_refined0.165
r_symmetry_nbtor_other0.076
r_chiral_restr0.066
r_symmetry_xyhbond_nbd_other0.032
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3628
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms87

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
STARANISOdata scaling
REFMACphasing