5LA7

Crystal structure of human proheparanase, in complex with glucuronic acid configured aziridine probe JJB355


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 Succinate pH 7.0 17% PEG3350 1:250 dilution seed stock Seed crystals grown in 0.2 M Ammonium Nitrate, 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2745.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.41α = 90
b = 88.02β = 90
c = 118.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.9450.411000.06616.56.539772
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)
11.941.991001.3161.56.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5e8m1.9449.1137718199199.960.18420.182050.22321RANDOM46.254
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]
-0.39-1.962.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.971
r_dihedral_angle_4_deg18.199
r_dihedral_angle_3_deg15.032
r_long_range_B_refined6.996
r_long_range_B_other6.996
r_dihedral_angle_1_deg6.727
r_scangle_other5.344
r_mcangle_it4.324
r_mcangle_other4.323
r_scbond_it3.518
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.971
r_dihedral_angle_4_deg18.199
r_dihedral_angle_3_deg15.032
r_long_range_B_refined6.996
r_long_range_B_other6.996
r_dihedral_angle_1_deg6.727
r_scangle_other5.344
r_mcangle_it4.324
r_mcangle_other4.323
r_scbond_it3.518
r_scbond_other3.506
r_mcbond_it3.092
r_mcbond_other3.086
r_angle_refined_deg1.607
r_angle_other_deg0.952
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4072
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms128

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing