5E9B

Crystal structure of human heparanase in complex with HepMer M09S05a


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 [5.5] 0.1 M MgCl2 17% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.99α = 90
b = 71.06β = 95.09
c = 78.29γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.850DiamondI03

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
11.8852.5299.80.0612.14.140880
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.931.01

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 REPLACEMENTTHROUGHOUT5e8m1.8852.5240866203699.7150.180.17810.2172taken from apo40.236
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]
1.8982.229-2.7320.431
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg15.807
r_dihedral_angle_3_deg14.304
r_lrange_it7.635
r_lrange_other7.634
r_dihedral_angle_1_deg6.987
r_scangle_it5.882
r_scangle_other5.881
r_mcangle_it4.48
r_mcangle_other4.479
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.114
r_dihedral_angle_4_deg15.807
r_dihedral_angle_3_deg14.304
r_lrange_it7.635
r_lrange_other7.634
r_dihedral_angle_1_deg6.987
r_scangle_it5.882
r_scangle_other5.881
r_mcangle_it4.48
r_mcangle_other4.479
r_scbond_other3.873
r_scbond_it3.87
r_mcbond_it3.192
r_mcbond_other3.192
r_angle_refined_deg1.581
r_angle_other_deg1.277
r_symmetry_nbd_refined0.269
r_nbd_other0.243
r_nbd_refined0.198
r_symmetry_nbd_other0.178
r_nbtor_refined0.167
r_xyhbond_nbd_refined0.164
r_symmetry_xyhbond_nbd_refined0.117
r_symmetry_nbtor_other0.077
r_chiral_restr0.071
r_symmetry_xyhbond_nbd_other0.012
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3643
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing