5E98

Crystal structure of human heparanase in complex with HepMer M04S02a


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1 M MES [5.5] 0.1 M MgCl2 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.79α = 90
b = 71.29β = 95.06
c = 77.92γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.6338.4599.50.0511.7461989
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)
11.631.671.0770.6250.4651.33.8

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5e8m1.6338.4561968308399.4540.1710.16970.2063from apo structure35.312
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]
1.140.351-1.096-0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.901
r_dihedral_angle_4_deg14.509
r_dihedral_angle_3_deg13.778
r_lrange_other8.205
r_lrange_it8.2
r_dihedral_angle_1_deg6.696
r_scangle_it6.442
r_scangle_other6.439
r_mcangle_it4.435
r_mcangle_other4.435
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.901
r_dihedral_angle_4_deg14.509
r_dihedral_angle_3_deg13.778
r_lrange_other8.205
r_lrange_it8.2
r_dihedral_angle_1_deg6.696
r_scangle_it6.442
r_scangle_other6.439
r_mcangle_it4.435
r_mcangle_other4.435
r_scbond_other4.352
r_scbond_it4.349
r_mcbond_it3.203
r_mcbond_other3.194
r_angle_refined_deg1.748
r_angle_other_deg1.412
r_nbd_other0.302
r_symmetry_nbd_refined0.269
r_nbd_refined0.235
r_symmetry_xyhbond_nbd_refined0.232
r_symmetry_nbd_other0.191
r_nbtor_refined0.174
r_xyhbond_nbd_refined0.165
r_chiral_restr0.084
r_symmetry_nbtor_other0.083
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3686
Nucleic Acid Atoms
Solvent Atoms243
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing